Methods and compositions for vaccination comprising nucleic acid and/or polypeptide sequences of chlamydia

ABSTRACT

The instant invention relates to antigens and nucleic acids encoding such antigens obtainable by screening a Chlamydia genome. In more specific aspects, the invention relates to methods of isolating such antigens and nucleic acids and to methods of using such isolated antigens for producing immune responses. The ability of an antigen to produce an immune response may be employed in vaccination or antibody preparation techniques.

[0001] The present application claims priority to co-pending U.S. Provisional Patent Application Serial No. 60/225,839 filed on Dec. 15, 2000. The entire text of the above-referenced disclosure is specifically incorporated herein by reference without disclaimer. The government owns rights in the present invention pursuant to DARPA grant number MDA 972-97-1-0013.

BACKGROUND OF THE INVENTION

[0002] 1. Field of the Invention

[0003] The present invention relates generally to the fields of immunology, bacteriology and molecular biology. More particularly, the invention relates to methods for screening and obtaining vaccines generated from the administration of expression libraries constructed from a Chlamydia psittaci genome or corresponding homologs from other Chlamydia species. In particular embodiments, it concerns methods and compositions for the vaccination of vertebrate animals against Chlamydia bacterial infections, wherein vaccination of the animal is via a protein or gene derived from part or all of the genes validated as vaccines.

[0004] 2. Description of Related Art

[0005] Intracellular bacteria of the genus Chlamydia are important pathogens in both man and vertebrate animals, causing blindness in man, sexually transmitted disease, and community-acquired pneumonia, and most likely act as co-factors in atherosclerotic plaque formation in human coronary heart disease.

[0006] Ubiquitous Chlamydia (C) psittaci infections in cattle cause mastitis, infertility and abortion. A primary economic impact of Chlamydia in dairy cattle is the loss of milk production and quality. Serological evidence for infection with ruminant Chlamydia psittaci is found in virtually all cattle (Kaltenbock et al., 1997). These infections typically do not cause overt signs of disease, but under stress of the host animal may elicit transient inflammation of the mammary gland and uterus. These stress-related herd health problems, while not clinically pronounced, result in major losses for animal agriculture due to reduced output and quality of animal products like milk.

[0007] Most existing vaccines for the treatment of bacterial infections are composed of live/attenuated or killed pathogens (Babiuk, 1999). Live/attenuated vaccines present the risk of residual, or reacquisition of, pathogenicity, and are associated with a high cost of production. In addition, efficacious live/attenuated vaccines cannot be developed against many pathogens, or are impractical to produce. Killed pathogens typically have less utility than live/attenuated vaccines, as they are not usually effective in eliciting cellular immune responses. An alternative is subunit vaccines that consist of one or a few proteins of the pathogen (Babiuk, 1999; Ellis, 1999). The proteins being developed for these vaccines are typically based on a dominant immune response in infected hosts, and/or on surmised importance in the disease process. Due to the high genetic complexity of bacteria or protozoa, the empirical approach to identify these proteins often requires extensive research on the pathogen's biology and produces a small, biased set of potential vaccine candidates. However, this is currently the only practical method when proteins are the commodity for testing a vaccine.

[0008] The development of genetic (DNA) immunization (Tang et al., 1992) not only offers a new method of vaccine delivery, but also enables a new, unbiased, approach to vaccine discovery. The inventors have proposed that the whole genome of a pathogen could be searched for protein vaccine candidates by directly assessing protection from challenge, termed expression library immunization (ELI) (U.S. Pat. No. 5,703,057, specifically incorporated herein by reference). It involves making an expression library representing the whole genome of the pathogen in a genetic immunization vector. The library is subdivided into smaller groups, and DNA from each library is used to vaccinate animals that are subsequently challenged. The advantage of this approach is that all of the potentially protective genes could be discovered and used in any useful combination to reconstitute a vaccine devoid of non-protective, immunopathological, or immunosuppressive antigens. The potential of ELI was demonstrated in a murine Mycoplasma pulmonis infection, against which random M. pulmonis libraries were protective (Barry et al., 1995). Since then, others have reported on protective libraries (Brayton et al., 1998; Piedrafita et al., 1999), but the reduction of these libraries to individual genes has not been demonstrated.

[0009] As described above, the widespread human and animal infections by the genus Chlamydia represents a particular challenge for vaccinology. Chlamydia psittaci infections in cattle cause mastitis, infertility and abortion. A primary economic impact of Chlamydia in dairy cattle is the loss of milk production and quality. Thus, an effective vaccine against Chlamydia bacterial infections in cattle would be of great economic importance. However, there presently have been no effective vaccines developed against any Chlamydia.

SUMMARY OF THE INVENTION

[0010] The present invention overcomes these difficulties and problems in the art and provides for methods of immunization using Chlamydia antigens and polynucleotides. The instant invention relates to antigens and nucleic acids encoding such antigens obtainable by screening a Chlamydia genome. In more specific aspects, the invention relates to methods of isolating such antigens and nucleic acids and to methods of using such isolated antigens for producing immune responses. The ability of an antigen to produce an immune response may be employed in vaccination or antibody preparation techniques.

[0011] In some embodiments, the invention relates to isolated polynucleotides having a region that comprises a sequence of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, or SEQ ID NO:68 a complement of any of these sequences, or fragments thereof, or sequences closely related to these sequences. In some more specific embodiments, the invention relates to such polynucleotides comprising a region having a sequence comprising at least 17, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 125, 150, 200, or more contiguous nucleotides in common with at least one of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, or SEQ ID NO:68 or its complement. Of course, such polynucleotides may comprise a region having all nucleotides in common with at least one of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, or SEQ ID NO:68 or its complement.

[0012] In another aspect, the invention relates to polypeptides having sequences of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, or SEQ ID NO:69 or fragments thereof, or sequences closely related to these sequences. The invention also relates to methods of producing such polypeptides using recombinant methods, for example, using the polynucleotides described above.

[0013] The invention relates to antibodies against Chlamydia psittaci antigens, including those directed against an antigen having sequences of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, or SEQ ID NO:69 or an antigenic fragment thereof, or sequences closely related to these sequences. The antibodies may be polyclonal or monoclonal and produced by methods known in the art.

[0014] The invention contemplates vaccines comprising: (a) a pharmaceutically acceptable carrier, and (b) at least one polynucleotide having a Chlamydia sequence. In presently preferred embodiments, the at least one polynucleotide has a Chlamydia psittaci, Chlamydia pneumoniae, Chlamydia trachomatis, or Chlamydia pecorum sequence. In some specific embodiments at least one polynucleotide has a Chlamydia psittaci or Chlamydia pneumonia sequence.

[0015] The at least one polynucleotide may be isolated from a Chlamydia genomic DNA expression library but it need not be. For example, the polynucleotide may also be a sequence from one species that is determined to be protective based on the protective ability of a homologous sequence in another species. For example, the polynucleotide could be a Chlamydia pneumonia sequence that was determined to be protective after analysis of the Chlamydia pneumonia genomic sequence for homologues of Chlamydia psittaci antigens that had previously been shown to be protective. As discussed below, the polynucleotides need not be of natural origin, or to encode an antigen that is precisely a naturally occurring Chlamydia antigen. It is anticipated that polynucleotides and antigens within the scope of this invention my be synthetic and/or engineered to mimic, or improve upon, naturally occurring polynucleotides and still be useful in the invention.

[0016] In some embodiments, the at least one polynucleotide has a sequence isolated from Chlamydia psittaci, for example, a sequence of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52:, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO: 58, or SEQ ID NO:60, or fragment thereof, or sequences closely related to these sequences. In more specific such embodiments, the at least one polynucleotide has a sequence of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, or SEQ ID NO:26, or fragment thereof, or sequences closely related to these sequences. In even more specific embodiments, the at least one polynucleotide has a sequence of SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:14, SEQ ID NO:20, or SEQ ID NO:24.

[0017] In some embodiments, the polynucleotide encodes an antigen having a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; or SEQ ID NO:69; or antigenic fragment thereof, or sequences closely related to these sequences.

[0018] In many embodiments, the polynucleotide is comprised in a genetic immunization vector. Such a vector may, but need not, comprise a gene encoding a mouse ubiquitin fusion polypeptide. The vector, in some preferred embodiments, will comprise a promoter operable in eukaryotic cells, for example, but not limited to a CMV promoter. Such promoters are well known to those of skill in the art. In some embodiments, the polynucleotide is comprised in a viral expression vector, for example, but not limited to, a vector selected from the group consisting of adenovirus, adeno-associated virus, retrovirus and herpes-simplex virus.

[0019] The vaccines of the invention may comprise multiple polynucleotide sequences from one or more Chlamydia species. In some embodiments, the vaccine will comprise at least a first polynucleotide having a Chlamydia psittaci sequence and a second polynucleotide having a sequence, wherein the first polynucleotide and the second polynucleotide have different sequences. In some more specific embodiments, the first polynucleotide may have a sequence of SEQ ID NO:50.

[0020] The present invention also involves vaccines comprising: (a) a pharmaceutically acceptable carrier; and (b) at least one Chlamydia antigen. The at least one Chlamydia antigen can be a Chlamydia psittaci, Chlamydia pneumoniae, Chlamydia trachomatis, or Chlamydia pecorum antigen or an antigen of any other Chlamydia species. In some cases, the at least one Chlamydia antigen is a Chlamydia psittaci antigen. In some embodiments, the at least one Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; or SEQ ID NO:69 or antigenic fragment thereof, or sequences closely related to these sequences. In some specific embodiments, the at least one Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, or SEQ ID NO:27, or an antigenic fragment thereof, or sequences closely related to these sequences. In even more specific embodiments, the at least one Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:11, SEQ ID NO:15, SEQ ID NO:21, or SEQ ID NO:25.

[0021] The invention also relates to methods of immunizing an animal comprising providing to the animal at least one Chlamydia antigen, or antigenic fragment thereof, in an amount effective to induce an immune response. Again, the at least one Chlamydia antigen can be of Chlamydia psittaci, Chlamydia pneumoniae, Chlamydia trachomatis, Chlamydia pecorum or any other Chlamydia species. In some cases, the at least one Chlamydia antigen is a Chlamydia psittaci antigen, while in others it will not be. In further examples the Chlamydia pneumoniae antigens are comprised of SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:675; SEQ ID NO:69: As discussed above, and described in detail below, the Chlamydia antigens useful in the invention need not be native antigens. Rather, these antigens may have sequences that have been modified in any number of ways known to those of skill in the art, so long as they result in or aid in an antigenic response.

[0022] In some embodiments of the invention, the provision of the at least one Chlamydia antigen comprises: (a) preparing a cloned expression library from fragmented genomic DNA, cDNA or sequenced genes of Chlamydia; (b) administering at least one clone of the library in a pharmaceutically acceptable carrier into the animal; and (c) expressing at least one Chlamydia antigen in the animal. The expression library may comprise at least one or more polynucleotides having a sequence of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO52:, SEQ ID NO.54, SEQ ID NO:56, SEQ ID NO:58, or SEQ ID NO:60, SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; or SEQ ID NO:68; or fragment thereof, or sequences closely related to these sequences. The expression library may be cloned in a genetic immunization vector, such as a vector of SEQ ID NO:1, or any other suitable vector. The vector may comprise a gene encoding a mouse ubiquitin fusion polypeptide designed to link the expression library polynucleotides to the ubiquitin gene. The vector may comprise a promoter operable in eukaryotic cells, for example a CMV promoter, or any other suitable promoter. In such methods, the polynucleotide may be administered by a intramuscular injection or epidermal injection. The polynucleotide may likewise be administered by intravenous, subcutaneous, intralesional, intraperitoneal, oral or inhaled routes of administration. In some specific, exemplary embodiments, the administration may be via intramuscular injection of at least 1.0 μg to 200 μg of the polynucleotide. In other exemplary embodiments, administration may be epidermal injection of at least 0.01 μg to 5.0 μg of the polynucleotide. In some cases, a second administration, for example, an intramuscular injection and/or epidermal injection, may administered at least about three weeks after the first administration. In these methods, the polynucleotide may be, but need not be, cloned into a viral expression vector, for example, a viral expression vector selected from the group consisting of adenovirus, herpes-simple virus, retrovirus and adeno-associated virus. The polynucleotide may also be administered in any other method disclosed herein or known to those of skill in the art.

[0023] In some embodiments, the provision of the Chlamydia antigen(s) may comprise: (a) preparing a pharmaceutical composition comprising at least one polynucleotide encoding a Chlamydia antigen or fragment thereof, (b) administering one or more clones of the library in a pharmaceutically acceptable carrier into the animal; and (c) expressing one or more Chlamydia antigens in the animal. The one or more polynucleotides can be comprised in one or more expression vectors, as described above and elsewhere in this specification.

[0024] Alternatively, the provision of the Chlamydia antigen(s) may comprise: (a) preparing a pharmaceutical composition of at least one Chlamydia antigen or an antigenic fragment thereof, and (b) administering the at least one antigen or fragment into the animal. The antigen(s) may be administered by a first intramuscular injection, intravenous injection, parenteral injection, epidermal injection, inhalation or oral route.

[0025] In preferred embodiments of the invention, the animal is a mammal. In some cases the mammal is a bovine, in others, the mammal is a human.

[0026] In some embodiments, these methods may induce an immune response against Chlamydia psittaci. Alternatively, these methods may be practiced in order to induce an immune response against a Chlamydia species other than Chlamydia psittaci, for example, but not limited to, Chlamydia pneumoniae, Chlamydia trachomatis, and/or Chlamydia pecorum. In some embodiments, these methods may be employed to induce an immune response against a non-Chlamydia infection or other disease.

[0027] These methods may comprise administering to the animal an antigen or antigenic fragment from a Chlamydia species other than Chlamydia psittaci. Also, these methods may comprise administering to the animal an antigen or antigenic fragment from a non-Chlamydia species.

[0028] This specification discusses methods of obtaining polynucleotide sequences effective for generating an immune response against the genus Chlamydia in a non-human animal comprising: (a) preparing a cloned expression library from fragmented genomic DNA of the genus Chlamydia; (b) administering one or more clones of the library in a pharmaceutically acceptable carrier into the animal in an amount effective to induce an immune response; and (c) selecting from the library the polynucleotide sequences that induce an immune response, wherein the immune response in the animal is protective against Chlamydia infection. Such methods may further comprise testing the animal for immune resistance against a Chlamydia bacterial infection by challenging the animal with Chlamydia. In some cases, the genomic DNA has been fragmented physically or by restriction enzymes, for example, but not limited to, fragments that average, about 200-1000 base pairs in length. In some cases, each clone in the library may comprise a gene encoding a mouse ubiquitin fusion polypeptide designed to link the expression library polynucleotides to the ubiquitin gene, but this is not required in all cases. In some cases, the library may comprise about 1×10³ to about 1×10⁶ clones; in more specific cases, the library could have 1×10⁵ clones. In some preferred methods, about 0.01 μg to about 200 μg of DNA, from the clones is administered into the animal. In some situations the genomic DNA, cDNA or sequenced gene is introduced by intramuscular injection or epidermal injection. In some versions of these protocols, the cloned expression library further comprises a promoter operably linked to the DNA that permits expression in a vertebrate animal cell.

[0029] The application also discloses methods of preparing antigens that confer protection against infection in a vertebrate animal comprising the steps of: (a) preparing a cloned expression library from fragmented genomic DNA of the genus Chlamydia; (b) administering one or more clones of the library in a pharmaceutically acceptable carrier into the animal in an amount effective to induce an immune response; (c) selecting from the library the polynucleotide sequences that induce an immune response and expressing the polynucleotide sequences in cell culture; and (d) purifying the polypeptide(s) expressed in the cell culture. Often, these methods further comprise testing the animal for immune resistance against infection by challenging the animal with one or more Chlamydia or other pathogens.

[0030] The invention relates to methods of preparing antibodies against a Chlamydia antigen comprising the steps of: (a) identifying a Chlamydia antigen that confers immune resistance against Chlamydia bacterial infection when challenged with the Chlamydia species in which the antigen was prepared; (b) generating an immune response in a vertebrate animal with the antigen identified in step (a); and (c) obtaining antibodies produced in the animal.

[0031] The invention also relates to methods of assaying for the presence of Chlamydia infection in a vertebrate animal comprising: (a) obtaining an antibody directed against a Chlamydia antigen; (b) obtaining a sample from the animal; (c) admixing the antibody with the sample; and (d) assaying the sample for antigen-antibody binding, wherein the antigen-antibody binding indicates Chlamydia infection in the animal. In some cases, the antibody directed against the antigen is further defined as a polyclonal antibody. In others, the antibody directed against the antigen is further defined as a monoclonal antibody. In some embodiments, the Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; or SEQ ID NO:69; or fragment thereof, or sequences closely related to these sequences. The assaying the sample for antigen-antibody binding may be by precipitation reaction, radioimmunoassay, ELISA, Western blot, immunofluorescence, or any other method known to those of skill in the art.

[0032] The invention also relates to kits for assaying a Chlamydia infection comprising, in a suitable container: (a) a pharmaceutically acceptable carrier; and (b) an antibody directed against a Chlamydia antigen.

[0033] The invention further relates to methods of assaying for the presence of a Chlamydia infection in an animal comprising: (a) obtaining an oligonucleotide probe comprising a sequence comprised within one of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO,12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO52:, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, or SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64; SEQ ID NO:66; or SEQ ID NO:68; or a complement thereof; and (b) employing the probe in a PCR or other detection protocol.

[0034] As used herein in the specification, “a” or “an” may mean one or more. As used herein, when used in conjunction with the word “comprising”, the words “a” or “an” may mean one or more than one. As used herein “another” may mean at least a second or more.

[0035] As used herein, “plurality” means more than one. In certain specific aspects, a plurality may mean 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 250, 300, 400, 500, 750, 1,000, 2,000, 3,000, 4,000, 5,000, 7,500, 10,000, 15,000, 20,000, 30,000, 40,000, 50,000, 60,000, 70,000, 80,000, 90,000, 100,000, 125,000, 150,000, 200,000 or more, and any integer derivable therein, and any range derivable therein.

[0036] As used herein, “any integer derivable therein” means a integer between the numbers described in the specification, and “any range derivable therein” means any range selected from such numbers or integers.

[0037] As used herein, a “fragment” refers to a sequence having or having at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000 or more contiguous residues of the recited SEQ ID NOS, but less than the full-length of the SEQ. ID. NOS. It is contemplated that the definition of “fragment” can be applied to amino acid and nucleic acid fragments.

[0038] As used herein, an “antigenic fragment” refers to a fragment, as defined above, that can elicit an immune response in an animal.

[0039] Reference to a sequence in an organism, such as a “Chlamydia sequence” refers to a segment of contiguous residues that is unique to that organism or that constitutes a fragment (or full-length region(s)) found in that organism (either amino acid or nucleic acid).

BRIEF DESCRIPTION OF THE DRAWINGS

[0040] The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

[0041]FIG. 1. Scheme for Expression Library Immunization.

[0042]FIG. 2. Production of the Chlamydia psittaci Library. The Chlamydia psittaci library was produced by first physically shearing the genomic DNA, strain BGM/B577, and size selecting fragments of 300-800 base pairs. The fragments were ligated into the Bgl II site of pCMVi-Ubs(+P3); see Sykes and Johnston, 1999 for details. The nucleotide sequence shown in this figure is given as SEQ ID NO:1.

[0043]FIG. 3. Flowchart depicting the process for deconvolution of the libraries. Each round consists of preparation of DNA samples, vaccination of mice, challenge and determination of the relative protection in each group.

[0044]FIG. 4. Results of protection assays in Rounds 1, 2 and 3. Protection was scored as lung weight relative to average of the vaccinated, maximum protection, positive control and the non-vaccinated, challenged, maximum disease, negative control. The relative protection score was calculated by assigning the score 1 to animals with lung weight equal to the vaccinated control and the score 0 to animals with lung weights equal to the challenged, non-vaccinated control. These points define a line; animals with lower lung weight, hence better protection, have a higher relative protection score. Animals that have worse disease than challenged, non-vaccinated controls, i.e. heavier lungs, will have a negative relative protection score. The unchallenged Naïve group consistently had lung weights slightly lower than the maximum protection, positive controls (Vaccinated) due to the peribronchiolar accumulation of lymphatic cells. In Rounds 2 and 3 the pools of plasmids from columns in the two-dimensional arrays are assigned numbers and the rows assigned letters. The solid bars indicate pools that were designated as protective and entered into the subsequent round. The error bars represent one standard deviation on either side of the mean.

[0045]FIG. 5. Results of protection assays of testing individual gene fragments in Round 4. Protection was scored as lung weight relative to the average of the vaccinated, maximum protection, positive control (Vaccinated=1) and the non-vaccinated, challenged, maximum disease, negative control (Challenged=0). The Pool<50AA is the DNA consisting of the pool of the 32 plasmids from Round 3 having predicted open-reading frames less than 50 amino acids long. Pool>50AA is the DNA consisting of all the 14 plasmids containing Chlamydia psittaci inserts encoding in-frame proteins more than 50 amino acids long. The numbers of each individual gene fragment tested correspond to the numbers in FIG. 4. The error bars represent one standard deviation of the mean.

[0046]FIG. 6. Summary of characterization of the single gene fragments of Round 4. The Relative Protection score of each Chlamydia psittaci (CP) gene fragment is provided along with the designation of the gene in Chlamydia pneumonia that has the highest similarity (Chlamydia pneumonia homologue). In two cases, gene fragment CP #4 and CP #12, the Chlamydia psittaci gene could also be identified. On the right is a linear map showing the location in each gene of the fragment that conferred protection (shaded).

[0047]FIG. 7. Protection data from DNA pools. CP1-6 is a negative pool from round 1. To test whether a single protective gene could be detected in a negative pool, 25 ng of either CP4 #4 or CP4 #11 was added to 50 μg of CP1-6.

[0048]FIG. 8. Protection against Chlamydia pneumoniae challenge by various homologs of Chlamydia pneumoniae from ELI-selected Chlamydia psittaci (CP) gene.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

[0049] The widespread human and animal infections by the genus Chlamydia represents a particular challenge for vaccinology. For example, Chlamydia psittaci infections in cattle cause mastitis, infertility and abortion. A primary economic impact of Chlamydia in dairy cattle is the loss of milk production and quality. Thus, an effective treatment for Chlamydia bacterial infections in human and other vertebrate animals would be of clinical and economic importance.

[0050] The present invention provides compositions and methods for the immunization of vertebrate animals, including humans, against infections using nucleic acid sequences and polypeptides elucidated by screening Chlamydia psittaci. These compositions and methods will be useful for immunization against Chlamydia psittaci bacterial infections and other infections and disease states. In particular embodiments, a vaccine composition directed against Chlamydia infections is provided. The vaccine according to the present invention comprises Chlamydia genes and polynucleotides identified by the inventors, that confer protective resistance in vertebrate animals to Chlamydia bacterial infections, and other infections. In other embodiments, the invention provides methods for immunizing an animal against Chlamydia infections, methods for preparing a cloned library via expression library immunization and methods for screening and identifying Chlamydia genes that confer protection against infection.

[0051] A. Expression Library Immunization

[0052] In particular embodiments, the immunization of vertebrate animals according to the present invention includes a cloned library of Chlamydia expression constructs. In specific embodiments, a cloned expression library of Chlamydia psittaci is provided. Expression library immunization, ELI herein, is well known in the art (U.S. Pat. No. 5,703,057, specifically incorporated herein by reference). In certain embodiments, the invention provides an ELI method applicable to virtually any pathogen and requires no knowledge of the biological properties of the pathogen. The method operates on the assumption, generally accepted by those skilled in the art, that all the potential antigenic determinants of any pathogen are encoded in its genome. The inventors have previously devised methods of identifying vaccines using a genomic expression library representing all of the antigenic determinants of a pathogen (U.S. Pat. No. 5,703,057). The method uses to its advantage the simplicity of genetic immunization to sort through a genome for immunological reagents in an unbiased, systematic fashion.

[0053] The preparation of an expression library is performed using the techniques and methods familiar one of skill in the art. The pathogen's genome, may or may not be known or possibly may even have been cloned. Thus one obtains DNA (or cDNA), representing substantially the entire genome of the pathogen (e.g., Chlamydia psittaci). The DNA is broken up, by physical fragmentation or restriction endonuclease, into segments of some length so as to provide a library of about 10⁵ (approximately 18× the genome size) members. The library is then tested by inoculating a subject with purified DNA of the library or sub-library and the subject challenged with a pathogen, wherein immune protection of the subject from pathogen challenge indicates a clone that confers a protective immune response against infection.

[0054] B. Nucleic Acids

[0055] The present invention provides Chlamydia polynucleotide compositions and methods that induce a protective immune response in vertebrate animals challenged with a Chlamydia bacterial infection. The preparation and purification of antigenic Chlamydia polypeptides, or fragments thereof (Section C) and antibody preparations directed against Chlamydia antigens, or fragments thereof (Section E) are described below.

[0056] Thus, in certain embodiments of the present invention, genes or polynucleotides encoding Chlamydia polypeptides or fragments thereof are provided. It is contemplated in other embodiments, that a polynucleotide encoding a Chlamydia polypeptide or polypeptide fragment will be expressed in prokaryotic or eukaryotic cells and the polypeptides purified for use as anti-Chlamydia antigens in the vaccination of vertebrate animals or in generating antibodies immunoreactive with Chlamydia polypeptides (i.e., antigens). The genomes of Chlamydia pneumoniae and Chlamydia trachomatis have been completely sequenced. The Chlamydia genes are quite similar, with the four most protective genes identified being 30-71% identical and 45-85% similar in amino acid sequence.

[0057] Genes for various species of the genus Chlamydia have been cloned, identified and compared (Kalman et al., 1999; Meijer et al., 1999). For example, the genomes of Chlamydia pneumoniae, Chlamydia trachomatis, Chlamydia psittaci and Chlamydia pecorum have been studied. The present invention is not limited in scope to the genes of Chlamydia psittaci, however, as one of ordinary skill in the art could, using these nucleic acids, readily identify related homologues in various other species. In addition, it should be clear that the present invention is not limited to the specific nucleic acids disclosed herein. As discussed below, a specific “Chlamydia” gene or polynucleotide fragment may contain a variety of different bases and yet still produce a corresponding polypeptide that is functionally indistinguishable, and in some cases structurally indistinguishable, from the polynucleotide sequences disclosed herein by reference in U.S. patent application Ser. No. 09/738,269 filed on Dec. 15, 2000.

[0058] 1. Nucleic Acids Encoding Chlamydia Polypeptides

[0059] The present invention provides polynucleotides encoding antigenic Chlamydia psittaci polypeptides capable of inducing a protective immune response in vertebrate animals and for use as an antigen to generate anti-Chlamydia psittaci or other pathogen antibodies. In certain instances, it may be desirable to express Chlamydia psittaci polynucleotides encoding a particular antigenic Chlamydia psittaci polypeptide domain or sequence to be used as a vaccine or in generating anti-Chlamydia psittaci or other pathogen antibodies. Nucleic acids according to the present invention may encode an entire Chlamydia psittaci gene, or any other fragment of the Chlamydia psittaci sequences set forth herein. The nucleic acid may be derived from genomic DNA, i.e., cloned directly from the genome of a particular organism. In other embodiments, however, the nucleic acid may comprise complementary DNA (cDNA). A protein may be derived from the designated sequences for use in a vaccine or to isolate useful antibodies.

[0060] The term “cDNA” is intended to refer to DNA prepared using messenger RNA (mRNA) as template. The advantage of using a cDNA, as opposed to genomic DNA or DNA polymerized from a genomic, non- or partially-processed RNA template, is that the cDNA primarily contains coding sequences of the corresponding protein. There may be times when the full or partial genomic sequence is preferred, such as where the non-coding regions are required for optimal expression.

[0061] It also is contemplated that a given Chlamydia polynucleotide from a given species may be represented by natural variants that have slightly different nucleic acid sequences but, nonetheless, encode the same polypeptide (see Table 2 below). In addition, it is contemplated that a given Chlamydia polypeptide from a species may be generated using alternate codons that result in a different nucleic acid sequence but encodes the same polypeptide.

[0062] As used in this application, the term “a nucleic acid encoding a Chlamydia polynucleotide” refers to a nucleic acid molecule that has been isolated free of total cellular nucleic acid. The term “functionally equivalent codon” is used herein to refer to codons that encode the same amino acid, such as the six codons for arginine or serine (Table 2, below), and also refers to codons that encode biologically equivalent amino acids, as discussed in the following pages. TABLE 1 Amino Acids Codons Alanine Ala A GCA GCC GCG GCU Cysteine Cys C UGC UGU Aspartic acid Asp D GAC GAU Glutamic acid Glu E GAA GAG Phenylalanine Phe F UUC UUU Glycine Gly G GGA GGC GGG GGU Histidine His H CAC CAU Isoleucine Ile I AUA AUC AUU Lysine Lys K AAA AAG Leucine Leu L UUA UUG CUA CUC CUG CUU Methionine Met M AUG Asparagine Asn N AAC AAU Proline Pro P CCA CCC CCG CCU Glutamine Gln Q CAA CAG Arginine Arg R AGA AGG CGA CGC CGG CGU Serine Ser S AGC AGU UCA UCC UCG UCU Threonine Thr T ACA ACC ACG ACU Valine Val V GUA GUC GUG GUU Tryptophan Trp W UGG Tyrosine Tyr Y UAC UAU

[0063] Allowing for the degeneracy of the genetic code, sequences that have at least about 50%, usually at least about 60%, more usually about 70%, most usually about 80%, preferably at least about 90% and most preferably about 95% of nucleotides that are identical to the nucleotides of given Chlamydia gene or polynucleotide. Sequences that are essentially the same as those set forth in a Chlamydia gene or polynucleotide may also be functionally defined as sequences that are capable of hybridizing to a nucleic acid segment containing the complement of a Chlamydia polynucleotide under standard conditions.

[0064] The DNA segments of the present invention include those encoding biologically functional equivalent Chlamydia proteins and peptides, as described above. Such sequences may arise as a consequence of codon redundancy and amino acid functional equivalency that are known to occur naturally within nucleic acid sequences and the proteins thus encoded. Alternatively, functionally equivalent proteins or peptides may be created via the application of recombinant DNA technology, in which changes in the protein structure may be engineered, based on considerations of the properties of the amino acids being exchanged. Changes designed by man may be introduced through the application of site-directed mutagenesis techniques or may be introduced randomly and screened later for the desired function, as described below.

[0065] 2. Oligonucleotide Sequences

[0066] Naturally, the present invention also encompasses DNA segments that are complementary, or essentially complementary to the sequences of a Chlamydia polynucleotide. Nucleic acid sequences that are “complementary” are those that are capable of base-pairing according to the standard Watson-Crick complementary rules. As used herein, the term “complementary sequences” means nucleic acid sequences that are substantially complementary, as may be assessed by the same nucleotide comparison set forth above, or as defined as being capable of hybridizing to the nucleic acid segment of a Chlamydia polynucleotide under relatively stringent conditions such as those described herein. Such sequences may encode the entire Chlamydia polypeptide or functional or non-functional fragments thereof.

[0067] Alternatively, the hybridizing segments may be shorter oligonucleotides. Sequences of 17 bases long should occur only once in the human genome and, therefore, suffice to specify a unique target sequence. Although shorter oligomers are easier to make and increase in vivo accessibility, numerous other factors are involved in determining the specificity of hybridization. Both binding affinity and sequence specificity of an oligonucleotide to its complementary target increases with increasing length. It is contemplated that exemplary oligonucleotides of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more base pairs will be used, although others are contemplated. Longer polynucleotides encoding 250, 500, 1000, 1212, 1500, 2000, 2500, 3000 or 3500 bases and longer are contemplated as well. Such oligonucleotides will find use, for example, as probes in Southern and Northern blots and as primers in amplification reactions, or for vaccines.

[0068] Suitable hybridization conditions will be well known to those of skill in the art. In certain applications, for example, substitution of amino acids by site-directed mutagenesis, it is appreciated that lower stringency conditions are required. Under these conditions, hybridization may occur even though the sequences of probe and target strand are not perfectly complementary, but are mismatched at one or more positions. Conditions may be rendered less stringent by increasing salt concentration and decreasing temperature. For example, a medium stringency condition could be provided by about 0.1 to 0.25 M NaCl at temperatures of about 37° C. to about 55° C., while a low stringency condition could be provided by about 0.15 M to about 0.9 M salt, at temperatures ranging from about 20° C. to about 55° C. Thus, hybridization conditions can be readily manipulated, and thus will generally be a method of choice depending on the desired results.

[0069] In other embodiments, hybridization may be achieved under conditions of, for example, 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl₂, 10 mM dithiothreitol, at temperatures between approximately 20° C. to about 37° C. Other hybridization conditions utilized could include approximately 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl₂, at temperatures ranging from approximately 40° C. to about 72° C. Formamide and SDS also may be used to alter the hybridization conditions.

[0070] One method of using probes and primers of the present invention is in the search for genes related to Chlamydia or, more particularly, homologues of Chlamydia from other species. Normally, the target DNA will be a genomic or cDNA library, although screening may involve analysis of RNA molecules. By varying the stringency of hybridization, and the region of the probe, different degrees of homology may be discovered.

[0071] Another way of exploiting probes and primers of the present invention is in site-directed, or site-specific mutagenesis. Site-specific mutagenesis is a technique useful in the preparation of individual peptides, or biologically functional equivalent proteins or peptides, through specific mutagenesis of the underlying DNA. The technique further provides a ready ability to prepare and test sequence variants, incorporating one or more of the foregoing considerations, by introducing one or more nucleotide sequence changes into the DNA. Site-specific mutagenesis allows the production of mutants through the use of specific oligonucleotide sequences which encode the DNA sequence of the desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a primer sequence of sufficient size and sequence complexity to form a stable duplex on both sides of the deletion junction being traversed. Typically, a primer of about 17 to 25 nucleotides in length is preferred, with about 5 to 10 residues on both sides of the junction of the sequence being altered.

[0072] The technique typically employs a bacteriophage vector that exists in both a single stranded and double stranded form. Typical vectors useful in site-directed mutagenesis include vectors such as the M13 phage. These phage vectors are commercially available and their use is generally well known to those skilled in the art. Double stranded plasmids are also routinely employed in site directed mutagenesis, which eliminates the step of transferring the gene of interest from a phage to a plasmid.

[0073] In general, site-directed mutagenesis is performed by first obtaining a single-stranded vector, or melting of two strands of a double stranded vector which includes within its sequence a DNA sequence encoding the desired protein. An oligonucleotide primer bearing the desired mutated sequence is synthetically prepared. This primer is then annealed with the single-stranded DNA preparation, taking into account the degree of mismatch when selecting hybridization conditions, and subjected to DNA polymerizing enzymes such as E. coli polymerase I Klenow fragment, in order to complete the synthesis of the mutation-bearing strand. Thus, a heteroduplex is formed wherein one strand encodes the original non-mutated sequence and the second strand bears the desired mutation. This heteroduplex vector is then used to transform appropriate cells, such as E. coli cells, and clones are selected that include recombinant vectors bearing the mutated sequence arrangement.

[0074] The preparation of sequence variants of the selected gene using site-directed mutagenesis is provided as a means of producing potentially useful species and is not meant to be limiting, as there are other ways in which sequence variants of genes may be obtained. For example, recombinant vectors encoding the desired gene may be treated with mutagenic agents, such as hydroxylamine, to obtain sequence variants.

[0075] C. Polypeptides and Antigens

[0076] For the purposes of the present invention a Chlamydia polypeptide used as an antigen may be a naturally-occurring Chlamydia polypeptide that has been extracted using protein extraction techniques well known to those of skill in the art. In particular embodiments, a Chlamydia antigen is identified by ELI and prepared in a pharmaceutically acceptable carrier for the vaccination of an animal against Chlamydia infection.

[0077] In alternative embodiments, the Chlamydia polypeptide or antigen may be a synthetic peptide. In still other embodiments, the peptide may be a recombinant peptide produced through molecular engineering techniques. The present section describes the methods and compositions involved in producing a composition of Chlamydia polypeptides for use as antigens in the present invention.

[0078] 1. Chlamydia Polypeptides as Antigens

[0079] Section A describes methods for preparing a cloned Chlamydia library via ELI. Described also are methods for screening and identifying Chlamydia genes that confer protection against Chlamydia infection. Thus, Chlamydia polypeptide encoding genes or their corresponding cDNA identified in the present invention can be inserted into an appropriate cloning vehicle for the production of Chlamydia polypeptides as antigens for the present invention. In addition, sequence variants of the polypeptide can be prepared. These may, for instance, be minor sequence variants of the polypeptide that arise due to natural variation within the population or they may be homologues found in other species. They also may be sequences that do not occur naturally, but that are sufficiently similar that they function similarly and/or elicit an immune response that cross-reacts with natural forms of the polypeptide. Sequence variants can be prepared by standard methods of site-directed mutagenesis such as those described below in the following section.

[0080] Another synthetic or recombinant variation of a Chlamydia-antigen is a polyepitopic moiety comprising repeats of epitopic determinants found naturally on Chlamydia proteins. Such synthetic polyepitopic proteins can be made up of several homomeric repeats of any one Chlamydia protein epitope; or can comprise of two or more heteromeric epitopes expressed on one or several Chlamydia protein epitopes.

[0081] Amino acid sequence variants of the polypeptide can be substitutional, insertional or deletion variants. Deletion variants lack one or more residues of the native protein which are not essential for function or immunogenic activity, and are exemplified by the variants lacking a transmembrane sequence described above. Another common type of deletion variant is one lacking secretory signal sequences or signal sequences directing a protein to bind to a particular part of a cell.

[0082] Substitutional variants typically contain the exchange of one amino acid for another at one or more sites within the protein, and may be designed to modulate one or more properties of the polypeptide such as stability against proteolytic cleavage. Substitutions preferably are conservative, that is, one amino acid is replaced with one of similar shape and charge. Conservative substitutions are well known in the art and include, for example, the changes of alanine to serine; arginine to lysine; asparagine to glutamine or histidine; aspartate to glutamate; cysteine to serine; glutamine to asparagine; glutamate to aspartate; glycine to proline; histidine to asparagine or glutamine; isoleucine to leucine or valine; leucine to valine or isoleucine; lysine to arginine; methionine to leucine or isoleucine; phenylalanine to tyrosine, leucine or methionine; serine to threonine; threonine to serine; tryptophan to tyrosine; tyrosine to tryptophan or phenylalanine; and valine to isoleucine or leucine.

[0083] Insertional variants include fusion proteins such as those used to allow rapid purification of the polypeptide and also can include hybrid proteins containing sequences from other proteins and polypeptides which are homologues of the polypeptide. For example, an insertional variant could include portions of the amino acid sequence of the polypeptide from one species, together with portions of the homologous polypeptide from another species. Other insertional variants can include those in which additional amino acids are introduced within the coding sequence of the polypeptide. These typically are smaller insertions than the fusion proteins described above and are introduced, for example, into a protease cleavage site.

[0084] In one embodiment, major antigenic determinants of the polypeptide may be identified by an empirical approach in which portions of the gene encoding the polypeptide are expressed in a recombinant host, and the resulting proteins tested for their ability to elicit an immune response. For example, the polymerase chain reaction (PCR) can be used to prepare a range of cDNAs encoding peptides lacking successively longer fragments of the C-terminus of the protein. The immunogenic activity of each of these peptides then identifies those fragments or domains of the polypeptide that are essential for this activity. Further experiments in which only a small number of amino acids are removed or added at each iteration then allows the location of other antigenic determinants of the polypeptide. Thus, the polymerase chain reaction, a technique for amplifying a specific segment of DNA via multiple cycles of denaturation-renaturation, using a thermostable DNA polymerase, deoxyribonucleotides and primer sequences is contemplated in the present invention (Mullis, 1990; Mullis et al., 1992).

[0085] Another embodiment for the preparation of the polypeptides according to the invention is the use of peptide mimetics. Mimetics are peptide-containing molecules that mimic elements of protein secondary structure. Because many proteins exert their biological activity via relatively small regions of their folded surfaces, their actions can be reproduced by much smaller designer (mimetic) molecules that retain the bioactive surfaces and have potentially improved pharmacokinetic/dynamic properties (Fairlie et al., 1998).

[0086] The underlying rationale behind the use of peptide mimetics is that the peptide backbone of proteins exists chiefly to orient amino acid side chains in such a way as to facilitate molecular interactions, such as those of antibody and antigen. However, unlike proteins, peptides often lack well defined three dimensional structure in aqueous solution and tend to be conformationally mobile. Progress has been made with the use of molecular constraints to stabilize the bioactive conformations. By affixing or incorporating templates that fix secondary and tertiary structures of small peptides, synthetic molecules (protein surface mimetics) can be devised to mimic the localized elements of protein structure that constitute bioactive surfaces. Methods for mimicking individual elements of secondary structure (helices, turns, strands, sheets) and for assembling their combinations into tertiary structures (helix bundles, multiple loops, helix-loop-helix motifs) have been reviewed (Fairlie et al., 1998; Moore, 1994).

[0087] Methods for predicting, preparing, modifying, and screening mimetic peptides are described in U.S. Pat. Nos. 5,933,819 and 5,869,451 (each specifically incorporated herein by reference). It is contemplated in the present invention, that peptide mimetics will be useful in screening modulators of an immune response.

[0088] Modifications and changes may be made in the structure of a gene and still obtain a functional molecule that encodes a protein or polypeptide with desirable characteristics. The following is a discussion based upon changing the amino acids of a protein to create an equivalent, or even an improved, second-generation molecule. The amino acid changes may be achieved by changing the codons of the DNA sequence, according to the following data.

[0089] For example, certain amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein's biological functional activity, certain amino acid substitutions can be made in a protein sequence, and its underlying DNA coding sequence, and nevertheless obtain a protein with like properties. It is thus contemplated by the inventor that various changes may be made in the DNA sequences of genes without appreciable loss of their biological utility or activity. Table 1 shows the codons that encode particular amino acids.

[0090] In making such changes, the hydropathic index of amino acids may be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte and Doolittle, 1982).

[0091] It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like.

[0092] Each amino acid has been assigned a hydropathic index on the basis of their hydrophobicity and charge characteristics (Kyte and Doolittle, 1982), these are: Isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9); and arginine (−4.5).

[0093] It is known in the art that certain amino acids may be substituted by other amino acids having a similar hydropathic index or score and still result in a protein with similar biological activity, i.e., still obtain a biological functionally equivalent protein. In making such changes, the substitution of amino acids whose hydropathic indices are within ±2 is preferred, those which are within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.

[0094] It also is understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity. U.S. Pat. No. 4,554,101, incorporated herein by reference, states that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with a biological property of the protein.

[0095] As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine *−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4).

[0096] It is understood that an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent and immunologically equivalent protein. In such changes, the substitution of amino acids whose hydrophilicity values are within ±2 is preferred, those that are within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.

[0097] As outlined above, amino acid substitutions generally are based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. Exemplary substitutions that take various of the foregoing characteristics into consideration are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.

[0098] 2. Synthetic Polypeptides

[0099] Contemplated in the present invention are Chlamydia Psittaci proteins and related peptides for use as antigens. In certain embodiments, the synthesis of a Chlamydia peptide fragment is considered. The peptides of the invention can be synthesized in solution or on a solid support in accordance with conventional techniques. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. See, for example, Stewart and Young, (1984); Tam et al., (1983); Merrifield, (1986); and Barany and Merrifield (1979), each incorporated herein by reference. Alternatively, recombinant DNA technology may be employed wherein a nucleotide sequence which encodes a peptide of the invention is inserted into an expression vector, transformed or transfected into an appropriate host cell and cultivated under conditions suitable for expression.

[0100] 3. Chlamydia Polypeptide/Antigen Purification

[0101] Chlamydia polypeptides, including Chlamydia psittaci polypeptides, of the present invention are used as antigens for inducing a protective immune response in an animal and for the preparation of anti-Chlamydia antibodies. Thus, certain aspects of the present invention concern the purification, and in particular embodiments, the substantial purification, of a Chlamydia polypeptide that is described herein above. The term “purified protein or peptide” as used herein, is intended to refer to a composition, isolatable from other components, wherein the protein or peptide is purified to any degree relative to its naturally-obtainable state. A purified protein or peptide therefore also refers to a protein or peptide, free from the environment in which it may naturally occur.

[0102] Generally, “purified” will refer to a protein or peptide composition that has been subjected to fractionation to remove various other components, and which composition substantially retains its expressed biological activity. Where the term “substantially purified” is used, this designation will refer to a composition in which the protein or peptide forms the major component of the composition, such as constituting about 50% or more of the proteins in the composition.

[0103] Various methods for quantifying the degree of purification of the protein or peptide will be known to those of skill in the art in light of the present disclosure. These include, for example, determining the specific activity of an active fraction, or assessing the number of polypeptides within a fraction by SDS/PAGE analysis. A preferred method for assessing the purity of a fraction is to calculate the specific activity of the fraction, to compare it to the specific activity of the initial extract, and to thus calculate the degree of purity, herein assessed by a “-fold purification number.” The actual units used to represent the amount of activity will, of course, be dependent upon the particular assay technique chosen to follow the purification and whether or not the expressed protein or peptide exhibits a detectable activity.

[0104] Various techniques suitable for use in protein purification will be well known to those of skill in the art. These include, for example, precipitation with ammonium sulphate, PEG, antibodies and the like or by heat denaturation, followed by centrifugation; chromatography steps such as ion exchange, gel filtration, reverse phase, hydroxylapatite and affinity chromatography; isoelectric focusing; gel electrophoresis; and combinations of such and other techniques. As is generally known in the art, it is believed that the order of conducting the various purification steps may be changed, or that certain steps may be omitted, and still result in a suitable method for the preparation of a substantially purified protein or peptide.

[0105] There is no general requirement that the protein or peptide always be provided in their most purified state. Indeed, it is contemplated that less substantially purified products will have utility in certain embodiments. Partial purification may be accomplished by using fewer purification steps in combination, or by utilizing different forms of the same general purification scheme. For example, it is appreciated that a cation-exchange column chromatography performed utilizing an HPLC apparatus will generally result in a greater-fold purification than the same technique utilizing a low pressure chromatography system. Methods exhibiting a lower degree of relative purification may have advantages in total recovery of protein product, or in maintaining the activity of an expressed protein.

[0106] It is known that the migration of a polypeptide can vary, sometimes significantly, with different conditions of SDS/PAGE (Capaldi et al., 1977). It will therefore be appreciated that under differing electrophoresis conditions, the apparent molecular weights of purified or partially purified expression products may vary.

[0107] High Performance Liquid Chromatography (BPLC) is characterized by a very rapid separation with extraordinary resolution of peaks. This is achieved by the use of very fine particles and high pressure to maintain and adequate flow rate. Separation can be accomplished in a matter of minutes, or a most an hour. Moreover, only a very small volume of the sample is needed because the particles are so small and close-packed that the void volume is a very small fraction of the bed volume. Also, the concentration of the sample need not be very great because the bands are so narrow that there is very little dilution of the sample.

[0108] Gel chromatography, or molecular sieve chromatography, is a special type of partition chromatography that is based on molecular size. The theory behind gel chromatography is that the column, which is prepared with tiny particles of an inert substance that contain small pores, separates larger molecules from smaller molecules as they pass through or around the pores, depending on their size. As long as the material of which the particles are made does not adsorb the molecules, the sole factor determining rate of flow is the size. Hence, molecules are eluted from the column in decreasing size, so long as the shape is relatively constant. Gel chromatography is unsurpassed for separating molecules of different size because separation is independent of all other factors such as pH, ionic strength, temperature, etc. There also is virtually no adsorption, less zone spreading and the elution volume is related in a simple matter to molecular weight.

[0109] Affinity Chromatography is a chromatographic procedure that relies on the specific affinity between a substance to be isolated and a molecule that it can specifically bind to. This is a receptor-ligand type interaction. The column material is synthesized by covalently coupling one of the binding partners to an insoluble matrix. The column material is then able to specifically adsorb the substance from the solution. Elution occurs by changing the conditions to those in which binding will not occur (alter pH, ionic strength, temperature, etc.).

[0110] D. Gene Delivery

[0111] In certain embodiments of the invention, an expression construct comprising a Chlamydia gene or other polynucleotide segment under the control of a heterologous promoter operable in eukaryotic cells is provided. For example, the delivery of Chlamydia psittaci, antigen-encoding expression constructs can be provided in this manner. The general approach in certain aspects of the present invention is to provide a cell with an expression construct encoding a specific protein, polypeptide or peptide fragment, thereby permitting the antigenic expression of the protein, polypeptide or peptide fragment to take effect in the cell. Following delivery of the expression construct, the protein, polypeptide or peptide fragment encoded by the expression construct is synthesized by the transcriptional and translational machinery of the cell, as well as any that may be provided by the expression construct.

[0112] Viral and non-viral vector systems are the two predominate categories for the delivery of an expression construct encoding a therapeutic protein, polypeptide, polypeptide fragment. Both vector systems are described in the following sections. There also are two primary approaches utilized in the delivery of an expression construct for the purposes of gene therapy; either indirect, ex vivo methods or direct, in vivo methods. Ex vivo gene transfer comprises vector modification of (host) cells in culture and the administration or transplantation of the vector modified cells to a gene therapy recipient. In vivo gene transfer comprises direct introduction of the vector (e.g., injection, inhalation) into the target source or therapeutic gene recipient.

[0113] In certain embodiments of the invention, the nucleic acid encoding the gene or polynucleotide may be stably integrated into the genome of the cell. In yet further embodiments, the nucleic acid may be stably or transiently maintained in the cell as a separate, episomal segment of DNA. Such nucleic acid segments or “episomes” encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. How the expression construct is delivered to a cell and/or where in the cell the nucleic acid remains is dependent on the type of vector employed. The following gene delivery methods provide the framework for choosing and developing the most appropriate gene delivery system for a preferred application.

[0114] 1. Non-Viral Polynucleotide Delivery

[0115] In one embodiment of the invention, a polynucleotide expression construct consists of naked recombinant DNA or plasmids. In preferred embodiments of the invention, an expression construct comprising, for example, a Chlamydia psittaci polynucleotide is administered to a subject via injection and/or particle bombardment (e.g., a gene gun). Thus, in one preferred embodiment, polynucleotide expression constructs are transferred into cells by accelerating DNA-coated microprojectiles to a high velocity, allowing the DNA-coated microprojectiles to pierce cell membranes and enter cells. In another preferred embodiment, polynucleotides are administered to a subject by injection. Injection of a polynucleotide expression construct may be given by intramuscular, intravenous, subcutaneous, ir intraperitoneal injection, as long as the polynucleotide expression construct can effectively be delivered to a desired target.

[0116] a. Particle Bombardment

[0117] Particle Bombardment depends on the ability to accelerate DNA-coated microprojectiles to a high velocity allowing them to pierce cell membranes and enter cells without killing them (Klein et al, 1987). Several devices for accelerating small particles have been developed. The most commonly used forms rely on high-pressure helium gas (Sanford et al., 1991), of which one of the present inventors is a co-inventor. The microprojectiles used have consisted of biologically inert substances such as tungsten or gold beads.

[0118] For microprojectile bombardment transformation using the constructs of the instant invention, both physical and biological parameters may be optimized. Physical factors are those that involve manipulating the DNA/microprojectile precipitate or those that affect the flight and velocity of either the macro- or microprojectiles. Biological factors include all steps involved in manipulation of cells before and immediately after bombardment, such as the osmotic adjustment of target cells to help alleviate the trauma associated with bombardment, the orientation of an immature embryo or other target tissue relative to the particle trajectory, and also the nature of the transforming DNA, such as linearized DNA or intact supercoiled plasmids.

[0119] Accordingly, it is contemplated that one may wish to adjust various bombardment parameters in small scale studies to fully optimize the conditions. One may particularly wish to adjust physical parameters such as DNA concentration, gap distance, flight distance, tissue distance, and helium pressure. It is further contemplated that the grade of helium may effect transformation efficiency. One also may optimize the trauma reduction factors (TRFs) by modifying conditions which influence the physiological state of the recipient cells and which may therefore influence transformation and integration efficiencies. For example, the osmotic state, tissue hydration and the subculture stage or cell cycle of the recipient cells may be adjusted for optimum transformation.

[0120] Other physical factors include those that involve manipulating the DNA/microprojectile precipitate or those that affect the flight and velocity of either the macro- or microprojectiles. Biological factors include all steps involved in manipulation of cells immediately before and after bombardment. The pre-bombardment culturing conditions, such as osmotic environment, the bombardment parameters, and the plasmid configuration have been adjusted to yield the maximum numbers of stable transformants.

[0121] For microprojectile bombardment, one will attach (i.e., “coat”) DNA to the microprojectiles such that it is delivered to recipient cells in a form suitable for transformation thereof. In this respect, at least some of the transforming DNA must be available to the target cell for transformation to occur, while at the same time during delivery the DNA must be attached to the microprojectile. Therefore, availability of the transforming DNA from the microprojectile may comprise the physical reversal of interactions between transforming DNA and the microprojectile following delivery of the microprojectile to the target cell. This need not be the case, however, as availability to a target cell may occur as a result of breakage of unbound segments of DNA or of other molecules which comprise the physical attachment to the microprojectile. Availability may further occur as a result of breakage of bonds between the transforming DNA and other molecules, which are either directly or indirectly attached to the microprojectile. It is further contemplated that transformation of a target cell may occur by way of direct illegitimate or homology-dependent recombination between the transforming DNA and the genomic DNA of the recipient cell. Therefore, as used herein, a “coated” microprojectile will be one which is capable of being used to transform a target cell, in that the transforming DNA will be delivered to the target cell, yet will be accessible to the target cell such that transformation may occur.

[0122] Any technique for coating microprojectiles which allows for delivery of transforming DNA to the target cells may be used. Methods for coating microprojectiles which have been demonstrated to work well with the current invention have been specifically disclosed herein. DNA may be bound to microprojectile particles using alternative techniques, however. For example, particles may be coated with streptavidin and DNA end labeled with long chain thiol cleavable biotinylated nucleotide chains. The DNA adheres to the particles due to the streptavidin-biotin interaction, but is released in the cell by reduction of the thiol linkage through reducing agents present in the cell.

[0123] Alternatively, particles may be prepared by functionalizing the surface of a gold oxide particle, providing free amine groups. DNA, having a strong negative charge, binds to the functionalized particles. Furthermore, charged particles may be deposited in controlled arrays on the surface of mylar flyer disks used in the PDS-1000 Biolistics device, thereby facilitating controlled distribution of particles delivered to target tissue.

[0124] b. Other Non-Viral Methods of Polynucleotide Delivery

[0125] Transfer of a cloned expression construct in the present invention also may be performed by any of the methods which physically or chemically permeabilize the cell membrane (e.g., calcium phosphate precipitation, DEAE-dextran, electroporation, direct microinjection, DNA-loaded liposomes and lipofectamine-DNA complexes, cell sonication, gene bombardment using high velocity microprojectiles and receptor-mediated transfection.

[0126] In certain embodiments, the use of lipid formulations and/or nanocapsules is contemplated for the introduction of a Chlamydia psittaci polynucleotide or polypeptide, or a gene therapy vector into host cells.

[0127] Nanocapsules can generally entrap compounds in a stable and/or reproducible way. To avoid side effects due to intracellular polymeric overloading, such ultrafine particles (sized around 0.1 μm) should be designed using polymers able to be degraded in vivo. Biodegradable polyalkyl-cyanoacrylate nanoparticles that meet these requirements are contemplated for use in the present invention, and/or such particles may be easily made.

[0128] In a preferred embodiment of the invention, the polynucleotide or polypeptide may be associated with a lipid. The polynucleotide or polypeptide associated with a lipid may be encapsulated in the aqueous interior of a liposome, interspersed within the lipid bilayer of a liposome, attached to a liposome via a linking molecule that is associated with both the liposome and the oligonucleotide, entrapped in a liposome, complexed with a liposome, dispersed in a solution containing a lipid, mixed with a lipid, combined with a lipid, contained as a suspension in a lipid, contained or complexed with a micelle, or otherwise associated with a lipid. The lipid or lipid/polynucleotide or polypeptide associated compositions of the present invention are not limited to any particular structure in solution. For example, they may be present in a bilayer structure, as micelles, or with a “collapsed” structure. They may also simply be interspersed in a solution, possibly forming aggregates which are not uniform in either size or shape.

[0129] Lipids suitable for use according to the present invention can be obtained from commercial sources. For example, dimyristyl phosphatidylcholine (“DMPC”) can be obtained from Sigma Chemical Co., dicetyl phosphate (“DCP”) is obtained from K & K Laboratories (Plainview, N.Y.); cholesterol (“Chol”) is obtained from Calbiochem-Behring; dimyristyl phosphatidylglycerol (“DMPG”) and other lipids may be obtained from Avanti Polar Lipids, Inc. (Birmingham, Ala.). Stock solutions of lipids in chloroform or chloroform/methanol can be stored at about −20° C. Preferably, chloroform is used as the only solvent since it is more readily evaporated than methanol.

[0130] “Liposome” is a generic term encompassing a variety of single and multilamellar lipid vehicles formed by the generation of enclosed lipid bilayers or aggregates. Liposomes may be characterized as having vesicular structures with a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh and Bachhawat, 1991). However, the present invention also encompasses compositions that have different structures in solution than the normal vesicular structure. For example, the lipids may assume a micellar structure or merely exist as non-uniform aggregates of lipid molecules. Also contemplated are lipofectamine-nucleic acid complexes.

[0131] Liposomes within the scope of the present invention can be prepared in accordance with known laboratory procedures, for example: the method of Bangham et al. (1965), the contents of which are incorporated herein by reference; the method of Gregoriadis, as described in DRUG CARRIERS IN BIOLOGY AND MEDICINE, G. Gregoriadis ed. (1979) pp. 287-341, the contents of which are incorporated herein by reference; the method of Deamer and Uster (1983), the contents of which are incorporated by reference; and the reverse-phase evaporation method as described by Szoka and Papahadjopoulos (1978).

[0132] Other vector delivery systems which can be employed to deliver a nucleic acid encoding a therapeutic gene into cells are receptor-mediated delivery vehicles. These take advantage of the selective uptake of macromolecules by receptor-mediated endocytosis in almost all eukaryotic cells. Because of the cell type-specific distribution of various receptors, the delivery can be highly specific (Wu and Wu, 1993).

[0133] Receptor-mediated gene targeting vehicles generally consist of two components: a cell receptor-specific ligand and a DNA-binding agent. Several ligands have been used for receptor-mediated gene transfer. The most extensively characterized ligands are asialoorosomucoid (ASOR) (Wu and Wu, 1987) and transferring (Wagner et al., 1990). Recently, a synthetic neoglycoprotein, which recognizes the same receptor as ASOR, has been used as a gene delivery vehicle (Ferkol et al., 1993; Perales et al., 1994) and epidermal growth factor (EGF) has also been used to deliver genes to squamous carcinoma cells (Myers, EPO 0273085).

[0134] In other embodiments, the delivery vehicle may comprise a ligand and a liposome. For example, Nicolau et al. (1987) employed lactosyl-ceramide, a galactose-terminal asialganglioside, incorporated into liposomes and observed an increase in the uptake of the insulin gene by hepatocytes. Thus, it is feasible that a nucleic acid encoding a therapeutic gene also may be specifically delivered into a cell type such as prostate, epithelial or tumor endothelial cells, by any number of receptor-ligand systems with or without liposomes. For example, the human prostate-specific antigen (Watt et al, 1986) may be used as the receptor for mediated delivery of a nucleic acid in prostate tissue.

[0135] In another embodiment of the invention, the expression construct may simply consist of naked recombinant DNA or plasmids. Transfer of the construct may be performed by any of the methods mentioned above which physically or chemically permeabilize the cell membrane. This is applicable particularly for transfer in vitro, however, it may be applied for in vivo use as well. Dubensky et al. (1984) successfully injected polyomavirus DNA in the form of CaPO₄ precipitates into liver and spleen of adult and newborn mice demonstrating active viral replication and acute infection. Benvenisty and Neshif (1986) also demonstrated that direct intraperitoneal injection of CaPO₄ precipitated plasmids results in expression of the transfected genes. It is envisioned that DNA encoding a Chlamydia psittaci gene or polynucleotide of interest may also be transferred in a similar manner in vivo and express the gene or polynucleotide product.

[0136] 2. Viral Vectors

[0137] In certain embodiments, it is contemplated that a Chlamydia psittaci gene or other polynucleotide that confers immune resistance to infection pursuant to the invention may be delivered by a viral vector. The capacity of certain viral vectors to efficiently infect or enter cells, to integrate into a host cell genome and stably express viral genes, have led to the development and application of a number of different viral vector systems (Robbins et al., 1998). Viral systems are currently being developed for use as vectors for ex vivo and in vivo gene transfer. For example, adenovirus, herpes-simple virus, retrovirus and adeno-associated virus vectors are being evaluated currently for treatment of diseases such as cancer, cystic fibrosis, Gaucher disease, renal disease and arthritis (Robbins and Ghivizzani, 1998; Imai et al., 1998; U.S. Pat. No. 5,670,488). The various viral vectors described below, present specific advantages and disadvantages, depending on the particular gene-therapeutic application.

[0138] a. Adenoviral Vectors

[0139] In particular embodiments, an adenoviral expression vector is contemplated for the delivery of expression constructs. “Adenovirus expression vector” is meant to include those constructs containing adenovirus sequences sufficient to (a) support packaging of the construct and (b) to ultimately express a tissue or cell-specific construct that has been cloned therein.

[0140] Adenoviruses comprise linear double stranded DNA, with a genome ranging from 30 to 35 kb in size (Reddy et al., 1998; Morrison et al., 1997; Chillon et al., 1999). An adenovirus expression vector according to the present invention comprises a genetically engineered form of the adenovirus. Advantages of adenoviral gene transfer include the ability to infect a wide variety of cell types, including non-dividing cells, a mid-sized genome, ease of manipulation, high infectivity and they can be grown to high titers (Wilson, 1996). Further, adenoviral infection of host cells does not result in chromosomal integration because adenoviral DNA can replicate in an episomal manner, without potential genotoxicity associated with other viral vectors. Adenoviruses also are structurally stable (Marienfeld et al., 1999) and no genome rearrangement has been detected after extensive amplification (Parks et al., 1997; Bett et al., 1993).

[0141] Salient features of the adenovirus genome are an early region (E1, E2, E3 and E4 genes), an intermediate region (pIX gene, Iva2 gene), a late region (L1, L2, L3, L4 and L5 genes), a major late promoter (MLP), inverted-terminal-repeats (ITRs) and a ψ sequence (Zheng, et al., 1999; Robbins et al., 1998; Graham and Prevec, 1995). The early genes E1, E2, E3 and E4 are expressed from the virus after infection and encode polypeptides that regulate viral gene expression, cellular gene expression, viral replication, and inhibition of cellular apoptosis. Further on during viral infection, the MLP is activated, resulting in the expression of the late (L) genes, encoding polypeptides required for adenovirus encapsidation. The intermediate region encodes components of the adenoviral capsid. Adenoviral inverted terminal repeats (ITRs; 100-200 bp in length), are cis elements, function as origins of replication and are necessary for viral DNA replication. The ψ sequence is required for the packaging of the adenoviral genome.

[0142] A common approach for generating an adenoviruses for use as a gene transfer vector is the deletion of the E1 gene (E1⁻), which is involved in the induction of the E2, E3 and E4 promoters (Graham and Prevec, 1995). Subsequently, a therapeutic gene or genes can be inserted recombinantly in place of the E1 gene, wherein expression of the therapeutic gene(s) is driven by the E1 promoter or a heterologous promoter. The E1⁻, replication-deficient virus is then proliferated in a “helper” cell line that provides the E1 polypeptides in trans (e.g., the human embryonic kidney cell line 293). Thus, in the present invention it may be convenient to introduce the transforming construct at the position from which the E1-coding sequences have been removed. However, the position of insertion of the construct within the adenovirus sequences is not critical to the invention. Alternatively, the E3 region, portions of the E4 region or both may be deleted, wherein a heterologous nucleic acid sequence under the control of a promoter operable in eukaryotic cells is inserted into the adenovirus genome for use in gene transfer (U.S. Pat. Nos. 5,670,488; 5,932,210, each specifically incorporated herein by reference).

[0143] Although adenovirus based vectors offer several unique advantages over other vector systems, they often are limited by vector immunogenicity, size constraints for insertion of recombinant genes and low levels of replication. The preparation of a recombinant adenovirus vector deleted of all open reading frames, comprising a full length dystrophin gene and the terminal repeats required for replication (Haecker et al., 1997) offers some potentially promising advantages to the above mentioned adenoviral shortcomings. The vector was grown to high titer with a helper virus in 293 cells and was capable of efficiently transducing dystrophin in mdx mice, in myotubes in vitro and muscle fibers in vivo. Helper-dependent viral vectors are discussed below.

[0144] A major concern in using adenoviral vectors is the generation of a replication-competent virus during vector production in a packaging cell line or during gene therapy treatment of an individual. The generation of a replication-competent virus could pose serious threat of an unintended viral infection and pathological consequences for the patient. Armentano et al., describe the preparation of a replication-defective adenovirus vector, claimed to eliminate the potential for the inadvertent generation of a replication-competent adenovirus (U.S. Pat. No. 5,824,544, specifically incorporated herein by reference). The replication-defective adenovirus method comprises a deleted E1 region and a relocated protein IX gene, wherein the vector expresses a heterologous, mammalian gene.

[0145] Other than the requirement that the adenovirus vector be replication defective, or at least conditionally defective, the nature of the adenovirus vector is not believed to be crucial to the successful practice of the invention. The adenovirus may be of any of the 42 different known serotypes and/or subgroups A-F. Adenovirus type 5 of subgroup C is the preferred starting material in order to obtain the conditional replication-defective adenovirus vector for use in the present invention. This is because adenovirus type 5 is a human adenovirus about which a great deal of biochemical and genetic information is known, and it has historically been used for most constructions employing adenovirus as a vector.

[0146] As stated above, the typical vector according to the present invention is replication defective and will not have an adenovirus E1 region. Adenovirus growth and manipulation is known to those of skill in the art, and exhibits broad host range in vitro and in vivo (U.S. Pat. Nos. 5,670,488; 5,932,210; 5,824,54). This group of viruses can be obtained in high titers, e.g., 10⁹ to 10¹¹ plaque-forming units per ml, and they are highly infective. The life cycle of adenovirus does not require integration into the host cell genome. The foreign genes delivered by adenovirus vectors are episomal and, therefore, have low genotoxicity to host cells. Many experiments, innovations, preclinical studies and clinical trials are currently under investigation for the use of adenoviruses as gene delivery vectors. For example, adenoviral gene delivery-based gene therapies are being developed for liver diseases (Han et al., 1999), psychiatric diseases (Lesch, 1999), neurological diseases (Smith, 1998; Hermens and Verhaagen, 1998), coronary diseases (Feldman et al., 1996), muscular diseases (Petrof, 1998), gastrointestinal diseases (Wu, 1998) and various cancers such as colorectal (Fujiwara and Tanaka, 1998; Dorai et al., 1999), pancreatic (Carrion et al., 1999), bladder (Irie et al., 1999), head and neck (Blackwell et al., 1999), breast (Stewart et al., 1999), lung (Batra et al., 1999) and ovarian (Vanderkwaak et al., 1999).

[0147] b. Retroviral Vectors

[0148] In certain embodiments of the invention, the use of retroviruses for gene delivery are contemplated. Retroviruses are RNA viruses comprising an RNA genome. When a host cell is infected by a retrovirus, the genomic RNA is reverse transcribed into a DNA intermediate which is integrated into the chromosomal DNA of infected cells. This integrated DNA intermediate is referred to as a provirus. A particular advantage of retroviruses is that they can stably infect dividing cells with a gene of interest (e.g., a therapeutic gene) by integrating into the host DNA, without expressing immunogenic viral proteins. Theoretically, the integrated retroviral vector will be maintained for the life of the infected host cell, expressing the gene of interest.

[0149] The retroviral genome and the proviral DNA have three genes: gag, pol, and env, which are flanked by two long terminal repeat (LTR) sequences. The gag gene encodes the internal structural (matrix, capsid, and nucleocapsid) proteins; the pol gene encodes the RNA-directed DNA polymerase (reverse transcriptase) and the env gene encodes viral envelope glycoproteins. The 5′ and 3′ LTRs serve to promote transcription and polyadenylation of the virion RNAs. The LTR contains all other cis-acting sequences necessary for viral replication.

[0150] A recombinant retrovirus of the present invention may be genetically modified in such a way that some of the structural, infectious genes of the native virus have been removed and replaced instead with a nucleic acid sequence to be delivered to a target cell (U.S. Pat. Nos. 5,858,744; 5,739,018, each incorporated herein by reference). After infection of a cell by the virus, the virus injects its nucleic acid into the cell and the retrovirus genetic material can integrate into the host cell genome. The transferred retrovirus genetic material is then transcribed and translated into proteins within the host cell. As with other viral vector systems, the generation of a replication-competent retrovirus during vector production or during therapy is a major concern. Retroviral vectors suitable for use in the present invention are generally defective retroviral vectors that are capable of infecting the target cell, reverse transcribing their RNA genomes, and integrating the reverse transcribed DNA into the target cell genome, but are incapable of replicating within the target cell to produce infectious retroviral particles (e.g., the retroviral genome transferred into the target cell is defective in gag, the gene encoding virion structural proteins, and/or in pol, the gene encoding reverse transcriptase). Thus, transcription of the provirus and assembly into infectious virus occurs in the presence of an appropriate helper virus or in a cell line containing appropriate sequences enabling encapsidation without coincident production of a contaminating helper virus.

[0151] The growth and maintenance of retroviruses is known in the art (U.S. Pat. Nos. 5,955,331; 5,888,502, each specifically incorporated herein by reference). Nolan et al. describe the production of stable high titre, helper-free retrovirus comprising a heterologous gene (U.S. Pat. No. 5,830,725, specifically incorporated herein by reference). Methods for constructing packaging cell lines useful for the generation of helper-free recombinant retroviruses with amphoteric or ecotrophic host ranges, as well as methods of using the recombinant retroviruses to introduce a gene of interest into eukaryotic cells in vivo and in vitro are contemplated in the present invention (U.S. Pat. No. 5,955,331).

[0152] Currently, the majority of all clinical trials for vector mediated gene delivery use murine leukemia virus (MLV)-based retroviral vector gene delivery (Robbins et al., 1998; Miller et al., 1993). Disadvantages of retroviral gene delivery includes a requirement for ongoing cell division for stable infection and a coding capacity that prevents the delivery of large genes. However, recent development of vectors such as lentivirus (e.g., HIV), simian immunodeficiency virus (SIV) and equine infectious-anemia virus (EIAV), which can infect certain non-dividing cells, potentially allow the in vivo use of retroviral vectors for gene therapy applications (Amado and Chen, 1999; Klimatcheva et al., 1999; White et al., 1999; Case et al., 1999). For example, HIV-based vectors have been used to infect non-dividing cells such as neurons (Takashi et al., 1999; Miyake et al., 1999), islets (Leibowitz et al., 1999) and muscle cells (Johnston et al., 1999). The therapeutic delivery of genes via retroviruses are currently being assessed for the treatment of various disorders such as inflammatory disease (Moldawer et al., 1999), AIDS (Amado et al., 1999; Engel and Kohn, 1999), cancer (Clay et al., 1999), cerebrovascular disease (Weihl et al., 1999) and hemophilia (Kay, 1998).

[0153] c. Herpes-Simplex Viral Vectors

[0154] Herpes simplex virus (HSV) type I and type II contain a double-stranded, linear DNA genome of approximately 150 kb, encoding 70-80 genes. Wild type HSV are able to infect cells lytically and to establish latency in certain cell types (e.g., neurons). Similar to adenovirus, HSV also can infect a variety of cell types including muscle (Yeung et al., 1999), ear (Derby et al., 1999), eye (Kaufman et al., 1999), tumors (Yoon et al., 1999; Howard et al., 1999), lung (Kohut et al., 1998), neuronal (Garrido et al., 1999; Lachmann and Efstathiou, 1999), liver (Miytake et al., 1999; Kooby et al., 1999) and pancreatic islets (Rabinovitch et al., 1999).

[0155] HSV viral genes are transcribed by cellular RNA polymerase II and are temporally regulated, resulting in the transcription and subsequent synthesis of gene products in roughly three discernable phases or kinetic classes. These phases of genes are referred to as the Immediate Early (IE) or alpha genes, Early (E) or beta genes and Late (L) or gamma genes. Immediately following the arrival of the genome of a virus in the nucleus of a newly infected cell, the IE genes are transcribed. The efficient expression of these genes does not require prior viral protein synthesis. The products of IE genes are required to activate transcription and regulate the remainder of the viral genome.

[0156] For use in therapeutic gene delivery, HSV must be rendered replication-defective. Protocols for generating replication-defective HSV helper virus-free cell lines have been described (U.S. Pat. Nos. 5,879,934; 5,851,826, each specifically incorporated herein by reference in its entirety). One IE protein, Infected Cell Polypeptide 4 (ICP4), also known as alpha 4 or Vmw175, is absolutely required for both virus infectivity and the transition from IE to later transcription. Thus, due to its complex, multifunctional nature and central role in the regulation of HSV gene expression, ICP4 has typically been the target of HSV genetic studies.

[0157] Phenotypic studies of HSV viruses deleted of ICP4 indicate that such viruses will be potentially useful for gene transfer purposes (Krisky et al., 1998a). One property of viruses deleted for ICP4 that makes them desirable for gene transfer is that they only express the five other IE genes: ICP0, ICP6, ICP27, ICP22 and ICP47 (DeLuca et al., 1985), without the expression of viral genes encoding proteins that direct viral DNA synthesis, as well as the structural proteins of the virus. This property is desirable for minimizing possible deleterious effects on host cell metabolism or an immune response following gene transfer. Further deletion of IE genes ICP22 and ICP27, in addition to ICP4, substantially improve reduction of HSV cytotoxicity and prevented early and late viral gene expression (Krisky et al., 1998b).

[0158] The therapeutic potential of HSV in gene transfer has been demonstrated in various in vitro model systems and in vivo for diseases such as Parkinson's (Yamada et al., 1999), retinoblastoma (Hayashi et al., 1999), intracerebral and intradermal tumors (Moriuchi et al., 1998), B cell malignancies (Suzuki et al., 1998), ovarian cancer (Wang et al., 1998) and Duchenne muscular dystrophy (Huard et al, 1997).

[0159] d. Adeno-associated Viral Vectors

[0160] Adeno-associated virus (AAV), a member of the parvovirus family, is a human virus that is increasingly being used for gene delivery therapeutics. AAV has several advantageous features not found in other viral systems. First, AAV can infect a wide range of host cells, including non-dividing cells. Second, AAV can infect cells from different species. Third, AAV has not been associated with any human or animal disease and does not appear to alter the biological properties of the host cell upon integration. For example, it is estimated that 80-85% of the human population has been exposed to AAV. Finally, AAV is stable at a wide range of physical and chemical conditions which lends itself to production, storage and transportation requirements.

[0161] The AAV genome is a linear, single-stranded DNA molecule containing 4681 nucleotides. The AAV genome generally comprises an internal non-repeating genome flanked on each end by inverted terminal repeats (ITRs) of approximately 145 bp in length. The ITRs have multiple functions, including origins of DNA replication, and as packaging signals for the viral genome. The internal non-repeated portion of the genome includes two large open reading frames, known as the AAV replication (rep) and capsid (cap) genes. The rep and cap genes code for viral proteins that allow the virus to replicate and package the viral genome into a virion. A family of at least four viral proteins are expressed from the AAV rep region, Rep 78, Rep 68, Rep 52, and Rep 40, named according to their apparent molecular weight. The AAV cap region encodes at least three proteins, VP1, VP2, and VP3.

[0162] AAV is a helper-dependent virus requiring co-infection with a helper virus (e.g., adenovirus, herpesvirus or vaccinia) in order to form AAV virions. In the absence of co-infection with a helper virus, AAV establishes a latent state in which the viral genome inserts into a host cell chromosome, but infectious virions are not produced. Subsequent infection by a helper virus “rescues” the integrated genome, allowing it to replicate and package its genome into infectious AAV virions. Although AAV can infect cells from different species, the helper virus must be of the same species as the host cell (e.g., human AAV will replicate in canine cells co-infected with a canine adenovirus).

[0163] AAV has been engineered to deliver genes of interest by deleting the internal non-repeating portion of the AAV genome and inserting a heterologous gene between the ITRs. The heterologous gene may be functionally linked to a heterologous promoter (constitutive, cell-specific, or inducible) capable of driving gene expression in target cells. To produce infectious recombinant AAV (rAAV) containing a heterologous gene, a suitable producer cell line is transfected with a rAAV vector containing a heterologous gene. The producer cell is concurrently transfected with a second plasmid harboring the AAV rep and cap genes under the control of their respective endogenous promoters or heterologous promoters. Finally, the producer cell is infected with a helper virus.

[0164] Once these factors come together, the heterologous gene is replicated and packaged as though it were a wild-type AAV genome. When target cells are infected with the resulting rAAV virions, the heterologous gene enters and is expressed in the target cells. Because the target cells lack the rep and cap genes and the adenovirus helper genes, the rAAV cannot further replicate, package or form wild-type AAV.

[0165] The use of helper virus, however, presents a number of problems. First, the use of adenovirus in a rAAV production system causes the host cells to produce both rAAV and infectious adenovirus. The contaminating infectious adenovirus can be inactivated by heat treatment (56.degree. C. for 1 hour). Heat treatment, however, results in approximately a 50% drop in the titer of functional rAAV virions. Second, varying amounts of adenovirus proteins are present in these preparations. For example, approximately 50% or greater of the total protein obtained in such rAAV virion preparations is free adenovirus fiber protein. If not completely removed, these adenovirus proteins have the potential of eliciting an immune response from the patient. Third, AAV vector production methods which employ a helper virus require the use and manipulation of large amounts of high titer infectious helper virus, which presents a number of health and safety concerns, particularly in regard to the use of a herpesvirus. Fourth, concomitant production of helper virus particles in rAAV virion producing cells diverts large amounts of host cellular resources away from rAAV virion production, potentially resulting in lower rAAV virion yields.

[0166] e. Other Viral Vectors

[0167] The development and utility of viral vectors for gene delivery is constantly improving and evolving. Other viral vectors such as poxvirus; e.g., vaccinia virus (Gnant et al., 1999; Gnant et al., 1999), alpha virus; e.g., sindbis virus, Semliki forest virus (Lundstrom, 1999), reovirus (Coffey et al., 1998) and influenza A virus (Neumann et al., 1999) are contemplated for use in the present invention and may be selected according to the requisite properties of the target system.

[0168] In certain embodiments, vaccinia viral vectors are contemplated for use in the present invention. Vaccinia virus is a particularly useful eukaryotic viral vector system for expressing heterologous genes. For example, when recombinant vaccinia virus is properly engineered, the proteins are synthesized, processed and transported to the plasma membrane. Vaccinia viruses as gene delivery vectors have recently been demonstrated to transfer genes to human tumor cells, e.g., EMAP-II (Gnant et al., 1999), inner ear (Derby et al., 1999), glioma cells, e.g., p53 (Timiryasova et al., 1999) and various mammalian cells, e.g., P-450 (U.S. Pat. No. 5,506,138). The preparation, growth and manipulation of vaccinia viruses are described in U.S. Pat. No. 5,849,304 and U.S. Pat. No. 5,506,138 (each specifically incorporated herein by reference).

[0169] In other embodiments, sindbis viral vectors are contemplated for use in gene delivery. Sindbis virus is a species of the alphavirus genus (Garoff and Li, 1998) which includes such important pathogens as Venezuelan, Western and Eastern equine encephalitis viruses (Sawai et al., 1999; Mastrangelo et al., 1999). In vitro, sindbis virus infects a variety of avian, mammalian, reptilian, and amphibian cells. The genome of sindbis virus consists of a single molecule of single-stranded RNA, 11,703 nucleotides in length. The genomic RNA is infectious, is capped at the 5′ terminus and polyadenylated at the 3′ terminus, and serves as mRNA. Translation of a vaccinia virus 26S mRNA produces a polyprotein that is cleaved co- and post-translationally by a combination of viral and presumably host-encoded proteases to give the three virus structural proteins, a capsid protein (C) and the two envelope glycoproteins (E1 and PE2, precursors of the virion E2).

[0170] Three features of sindbis virus suggest that it would be a useful vector for the expression of heterologous genes. First, its wide host range, both in nature and in the laboratory. Second, gene expression occurs in the cytoplasm of the host cell and is rapid and efficient. Third, temperature-sensitive mutations in RNA synthesis are available that may be used to modulate the expression of heterologous coding sequences by simply shifting cultures to the non-permissive temperature at various time after infection. The growth and maintenance of sindbis virus is known in the art (U.S. Pat. No. 5,217,879, specifically incorporated herein by reference).

[0171] f. Chimeric Viral Vectors

[0172] Chimeric or hybrid viral vectors are being developed for use in therapeutic gene delivery and are contemplated for use in the present invention. Chimeric poxviral/retroviral vectors (Holzer et al., 1999), adenoviral/retroviral vectors (Feng et al., 1997; Bilbao et al., 1997; Caplen et al., 1999) and adenoviral/adeno-associated viral vectors (Fisher et al., 1996; U.S. Pat. No. 5,871,982) have been described.

[0173] These “chimeric” viral gene transfer systems can exploit the favorable features of two or more parent viral species. For example, Wilson et al., provide a chimeric vector construct which comprises a portion of an adenovirus, AAV 5′ and 3′ ITR sequences and a selected transgene, described below (U.S. Pat. No. 5,871,983, specifically incorporate herein by reference).

[0174] The adenovirus/AAV chimeric virus uses adenovirus nucleic acid sequences as a shuttle to deliver a recombinant AAV/transgene genome to a target cell. The adenovirus nucleic acid sequences employed in the hybrid vector can range from a minimum sequence amount, which requires the use of a helper virus to produce the hybrid virus particle, to only selected deletions of adenovirus genes, which deleted gene products can be supplied in the hybrid viral production process by a selected packaging cell. At a minimum, the adenovirus nucleic acid sequences employed in the pAdA shuttle vector are adenovirus genomic sequences from which all viral genes are deleted and which contain only those adenovirus sequences required for packaging adenoviral genomic DNA into a preformed capsid head. More specifically, the adenovirus sequences employed are the cis-acting 5′ and 3′ inverted terminal repeat (ITR) sequences of an adenovirus (which function as origins of replication) and the native 5′ packaging/enhancer domain, that contains sequences necessary for packaging linear Ad genomes and enhancer elements for the E1 promoter. The adenovirus sequences may be modified to contain desired deletions, substitutions, or mutations, provided that the desired function is not eliminated.

[0175] The AAV sequences useful in the above chimeric vector are the viral sequences from which the rep and cap polypeptide encoding sequences are deleted. More specifically, the AAV sequences employed are the cis-acting 5′ and 3′ inverted terminal repeat (ITR) sequences. These chimeras are characterized by high titer transgene delivery to a host cell and the ability to stably integrate the transgene into the host cell chromosome (U.S. Pat. No. 5,871,983, specifically incorporate herein by reference). In the hybrid vector construct, the AAV sequences are flanked by the selected adenovirus sequences discussed above. The 5′ and 3′ AAV ITR sequences themselves flank a selected transgene sequence and associated regulatory elements, described below. Thus, the sequence formed by the transgene and flanking 5′ and 3′ AAV sequences may be inserted at any deletion site in the adenovirus sequences of the vector. For example, the AAV sequences are desirably inserted at the site of the deleted E1a/E1b genes of the adenovirus. Alternatively, the AAV sequences may be inserted at an E3 deletion, E2a deletion, and so on. If only the adenovirus 5′ ITR/packaging sequences and 3′ ITR sequences are used in the hybrid virus, the AAV sequences are inserted between them.

[0176] The transgene sequence of the vector and recombinant virus can be a gene, a nucleic acid sequence or reverse transcript thereof, heterologous to the adenovirus sequence, which encodes a protein, polypeptide or peptide fragment of interest. The transgene is operatively linked to regulatory components in a manner which permits transgene transcription. The composition of the transgene sequence will depend upon the use to which the resulting hybrid vector will be put. For example, one type of transgene sequence includes a therapeutic gene which expresses a desired gene product in a host cell. These therapeutic genes or nucleic acid sequences typically encode products for administration and expression in a patient in vivo or ex vivo to replace or correct an inherited or non-inherited genetic defect or treat an epigenetic disorder or disease.

[0177] E. Chlamydia Antibodies

[0178] In another aspect, the present invention provides antibody compositions that are immunoreactive with a Chlamydia polypeptide of the present invention, or any portion thereof.

[0179] An antibody can be a polyclonal or a monoclonal antibody. An antibody may also be monovalent or bivalent. A prototype antibody is an immunoglobulin composed by four polypeptide chains, two heavy and two light chains, held together by disulfide bonds. Each pair of heavy and light chains forms an antigen binding site, also defined as complementarity-determining region (CDR). Therefore, the prototype antibody has two CDRs, can bind two antigens, and because of this feature is defined bivalent. The prototype antibody can be split by a variety of biological or chemical means. Each half of the antibody can only bind one antigen and, therefore, is defined monovalent. Means for preparing and characterizing antibodies are well known in the art (see, e.g., Howell and Lane, 1988).

[0180] Peptides corresponding to one or more antigenic determinants of a Chlamydia polypeptide of the present invention also can be prepared. Such peptides should generally be at least five or six amino acid residues in length, will preferably be about 10, 15, 20, 25 or about 30 amino acid residues in length, and may contain up to about 35-50 residues or so. Synthetic peptides will generally be about 35 residues long, which is the approximate upper length limit of automated peptide synthesis machines, such as those available from Applied Biosystems (Foster City, Calif.). Longer peptides also may be prepared, e.g., by recombinant means.

[0181] The identification and preparation of epitopes from primary amino acid sequences on the basis of hydrophilicity is taught in U.S. Pat. No. 4,554,101 (Hopp), incorporated herein by reference. Through the methods disclosed in Hopp, one of skill in the art would be able to identify epitopes from within an amino acid sequence such as a Chlamydia polypeptide sequence.

[0182] Numerous scientific publications have also been devoted to the prediction of secondary structure, and to the identification of epitopes, from analyses of amino acid sequences (Chou & Fasman, 1974a; Chou & Fasman, 1974b; Chou & Fasman, 1978a; Chou & Fasman, 1978b; Chou & Fasman, 1979). Any of these may be used, if desired, to supplement the teachings of Hopp in U.S. Pat. No. 4,554,101.

[0183] Moreover, computer programs are currently available to assist with predicting antigenic portions and epitopic core regions of proteins. Examples include those programs based upon the Jameson-Wolf analysis (Jameson & Wolf, 1988; Wolf et al., 1988), the program PEPPLOT® (Brutlag et al., 1990; Weinberger et al., 1985), and other new programs for protein tertiary structure prediction (Fetrow & Bryant, 1993). Another commercially available software program capable of carrying out such analyses is MACVECTOR (IBI, New Haven, Conn.).

[0184] In further embodiments, major antigenic determinants of a Chlamydia polypeptide may be identified by an empirical approach in which portions of the gene encoding the polypeptide are expressed in a recombinant host, and the resulting proteins tested for their ability to elicit an immune response. For example, PCR can be used to prepare a range of peptides lacking successively longer fragments of the C-terminus of the protein. The immunoactivity of each of these peptides is determined to identify those fragments or domains of the polypeptide that are immunodominant. Further studies in which only a small number of amino acids are removed at each iteration then allows the location of the antigenic determinants of the polypeptide to be more precisely determined.

[0185] Another method for determining the major antigenic determinants of a polypeptide is the SPOTS system (Genosys Biotechnologies, Inc., The Woodlands, Tex.). In this method, overlapping peptides are synthesized on a cellulose membrane, which following synthesis and deprotection, is screened using a polyclonal or monoclonal antibody. The antigenic determinants of the peptides which are initially identified can be further localized by performing subsequent syntheses of smaller peptides with larger overlaps, and by eventually replacing individual amino acids at each position along the immunoreactive peptide.

[0186] Once one or more such analyses are completed, polypeptides are prepared that contain at least the essential features of one or more antigenic determinants. The peptides are then employed in the generation of antisera against the polypeptide. Minigenes or gene fusions encoding these determinants also can be constructed and inserted into expression vectors by standard methods, for example, using PCR cloning methodology.

[0187] The use of such small peptides for antibody generation or vaccination typically requires conjugation of the peptide to an immunogenic carrier protein, such as hepatitis B surface antigen, keyhole limpet hemocyanin or bovine serum albumin. Methods for performing this conjugation are well known in the art.

[0188] 1. Anti-Chlamydia Antibody Generation

[0189] The present invention provides monoclonal antibody compositions that are immunoreactive with a Chlamydia polypeptide. As detailed above, in addition to antibodies generated against a full length Chlamydia polypeptide, antibodies also may be generated in response to smaller constructs comprising epitopic core regions, including wild-type and mutant epitopes. In other embodiments of the invention, the use of anti-Chlamydia single chain antibodies, chimeric antibodies, diabodies and the like are contemplated.

[0190] As used herein, the term “antibody” is intended to refer broadly to any immunologic binding agent such as IgG, IgM, IgA, IgD and IgE. Generally, IgG and/or IgM are preferred because they are the most common antibodies in the physiological situation and because they are most easily made in a laboratory setting.

[0191] Monoclonal antibodies (mAbs) are recognized to have certain advantages, e.g., reproducibility and large-scale production, and their use is generally preferred.

[0192] However, “humanized” Chlamydia antibodies also are contemplated, as are chimeric antibodies from mouse, rat, goat or other species, fusion proteins, single chain antibodies, diabodies, bispecific antibodies, and other engineered antibodies and fragments thereof. As defined herein, a “humanized” antibody comprises constant regions from a human antibody gene and variable regions from a non-human antibody gene. A “chimeric antibody, comprises constant and variable regions from two genetically distinct individuals. An anti-Chlamydia humanized or chimeric antibody can be genetically engineered to comprise a Chlamydia antigen binding site of a given of molecular weight and biological lifetime, as long as the antibody retains its Chlamydia antigen binding site.

[0193] The term “antibody” is used to refer to any antibody-like molecule that has an antigen binding region, and includes antibody fragments such as Fab′, Fab, F(ab′)₂, single domain antibodies (DABs), Fv, scFv (single chain Fv), chimeras and the like. Methods and techniques of producing the above antibody-based constructs and fragments are well known in the art (U.S. Pat. Nos. 5,889,157; 5,821,333; 5,888,773, each specifically incorporated herein by reference).

[0194] U.S. Pat. No. 5,889,157 describes a humanized B3 scFv antibody preparation. The B3 scFv is encoded from a recombinant, fused DNA molecule, that comprises a DNA sequence encoding humanized Fv heavy and light chain regions of a B3 antibody and a DNA sequence that encodes an effector molecule. The effector molecule can be any agent having a particular biological activity which is to be directed to a particular target cell or molecule. Described in U.S. Pat. No. 5,888,773, is the preparation of scFv antibodies produced in eukaryotic cells, wherein the scFv antibodies are secreted from the eukaryotic cells into the cell culture medium and retain their biological activity. It is contemplated that similar methods for preparing multi-functional anti-Chlamydia fusion proteins, as described above, may be utilized in the present invention.

[0195] Means for preparing and characterizing antibodies also are well known in the art (See, e.g., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; incorporated herein by reference). The methods for generating monoclonal antibodies (mAbs) generally begin along the same lines as those for preparing polyclonal antibodies. Briefly, a polyclonal antibody is prepared by immunizing an animal with an immunogenic Chlamydia polypeptide composition in accordance with the present invention and collecting antisera from that immunized animal.

[0196] A wide range of animal species can be used for the production of antisera. Typically the animal used for production of antisera is a rabbit, a mouse, a rat, a hamster, a guinea pig or a goat. Because of the relatively large blood volume of rabbits, a rabbit is a preferred choice for production of polyclonal antibodies.

[0197] As is well known in the art, a given composition may vary in its immunogenicity. It is often necessary therefore to boost the host immune system, as may be achieved by coupling a peptide or polypeptide immunogen to a carrier. Exemplary and preferred carriers are keyhole limpet hemocyanin (KLH) and bovine serum albumin (BSA). Other albumins such as ovalbumin, mouse serum albumin or rabbit serum albumin also can be used as carriers. Means for conjugating a polypeptide to a carrier protein are well known in the art and include glutaraldehyde, m-maleimidobenzoyl-N-hydroxysuccinimide ester, carboduimide and bis-biazotized benzidine.

[0198] As also well known in the art, the immunogenicity of a particular immunogen composition can be enhanced by the use of non-specific stimulators of the immune response, known as adjuvants. Suitable molecule adjuvants include all acceptable immunostimulatory compounds, such as cytokines, toxins or synthetic compositions.

[0199] Adjuvants that may be used include IL-1, IL-2, IL-4, IL-7, IL-12, γ-interferon, GMCSP, BCG, aluminum hydroxide, MDP compounds, such as thur-MDP and nor-MDP, CGP (MTP-PE), lipid A, and monophosphoryl lipid A (MPL). RIBI, which contains three components extracted from bacteria, MPL, trehalose dimycolate (TDM) and cell wall skeleton (CWS) in a 2% squalene/Tween 80 emulsion also is contemplated. MHC antigens may even be used. Exemplary, often preferred adjuvants include complete Freund's adjuvant (a non-specific stimulator of the immune response containing killed Mycobacterium tuberculosis), incomplete Freund's adjuvants and aluminum hydroxide adjuvant.

[0200] In addition to adjuvants, it may be desirable to coadminister biologic response modifiers (BRM), which have been shown to upregulate T cell immunity or downregulate suppressor cell activity. Such BRMs include, but are not limited to, Cimetidine (CIM; 1200 mg/d) (SmithKline Beecham, Pa.); low-dose Cyclophosphamide (CYP; 300 mg/m²) (Johnson/Mead, N.J.), cytokines such as γ-interferon, IL-2, or IL-12 or genes encoding proteins involved in immune helper functions, such as B-7.

[0201] The amount of immunogen composition used in the production of polyclonal antibodies varies upon the nature of the immunogen as well as the animal used for immunization. A variety of routes can be used to administer the immunogen (subcutaneous, intramuscular, intradermal, intravenous and intraperitoneal). The production of polyclonal antibodies may be monitored by sampling blood of the immunized animal at various points following immunization.

[0202] A second, booster injection, also may be given. The process of boosting and titering is repeated until a suitable titer is achieved. When a desired level of immunogenicity is obtained, the immunized animal can be bled and the serum isolated and stored, and/or the animal can be used to generate mAbs.

[0203] For production of rabbit polyclonal antibodies, the animal can be bled through an ear vein or alternatively by cardiac puncture. The removed blood is allowed to coagulate and then centrifuged to separate serum components from whole cells and blood clots. The serum may be used as is for various applications or else the desired antibody fraction may be purified by well-known methods, such as affinity chromatography using another antibody, a peptide bound to a solid matrix, or by using, e.g., protein A or protein G chromatography.

[0204] mAbs may be readily prepared through use of well-known techniques, such as those exemplified in U.S. Pat. No. 4,196,265, incorporated herein by reference. Typically, this technique involves immunizing a suitable animal with a selected immunogen composition, e.g., a purified or partially purified Chlamydia polypeptide, peptide or domain, be it a wild-type or mutant composition. The immunizing composition is administered in a manner effective to stimulate antibody producing cells.

[0205] The methods for generating monoclonal antibodies (mAbs) generally begin along the same lines as those for preparing polyclonal antibodies. Rodents such as mice and rats are preferred animals, however, the use of rabbit, sheep or frog cells also is possible. The use of rats may provide certain advantages (Goding, 1986, pp. 60-61), but mice are preferred, with the BALB/c mouse being most preferred as this is most routinely used and generally gives a higher percentage of stable fusions.

[0206] The animals are injected with antigen, generally as described above. The antigen may be coupled to carrier molecules such as keyhole limpet hemocyanin if necessary. The antigen would typically be mixed with adjuvant, such as Freund's complete or incomplete adjuvant. Booster injections with the same antigen would occur at approximately two-week intervals, or the gene encoding the protein of interest can be directly injected.

[0207] Following immunization, somatic cells with the potential for producing antibodies, specifically B lymphocytes (B cells), are selected for use in the mAb generating protocol. These cells may be obtained from biopsied spleens, tonsils or lymph nodes, or from a peripheral blood sample. Spleen cells and peripheral blood cells are preferred, the former because they are a rich source of antibody-producing cells that are in the dividing plasmablast stage, and the latter because peripheral blood is easily accessible.

[0208] Often, a panel of animals will have been immunized and the spleen of an animal with the highest antibody titer will be removed and the spleen lymphocytes obtained by homogenizing the spleen with a syringe. Typically, a spleen from an immunized mouse contains approximately 5×10⁷ to 2×10⁸ lymphocytes.

[0209] The antibody-producing B lymphocytes from the immunized animal are then fused with cells of an immortal myeloma cell, generally one of the same species as the animal that was immunized. Myeloma cell lines suited for use in hybridoma-producing fusion procedures preferably are non-antibody-producing, have high fusion efficiency, and enzyme deficiencies that render then incapable of growing in certain selective media which support the growth of only the desired fused cells (hybridomas).

[0210] Any one of a number of myeloma cells may be used, as are known to those of skill in the art (Goding, pp. 65-66, 1986; Campbell, pp. 75-83, 1984). For example, where the immunized animal is a mouse, one may use P3-X63/Ag8, X63-Ag8.653, NS1/1.Ag 4 1, Sp210-Ag14, FO, NSO/U, MPC-11, MPC11-X45-GTG 1.7 and S194/5XX0 Bul; for rats, one may use R210.RCY3, Y3-Ag 1.2.3, IR983F and 4B210; and U-266, GM1500-GRG2, LICR-LON-HMy2 and UC729-6 are all useful in connection with human cell fusions.

[0211] One preferred murine myeloma cell is the NS-1 myeloma cell line (also termed P3-NS-1-Ag4-1), which is readily available from the NIGMS Human Genetic Mutant Cell Repository by requesting cell line repository number GM3573. Another mouse myeloma cell line that may be used is the 8-azaguanine-resistant mouse murine myeloma SP2/0 non-producer cell line.

[0212] Methods for generating hybrids of antibody-producing spleen or lymph node cells and myeloma cells usually comprise mixing somatic cells with myeloma cells in a 2:1 proportion, though the proportion may vary from about 20:1 to about 1:1, respectively, in the presence of an agent or agents (chemical or electrical) that promote the fusion of cell membranes. Fusion methods using Sendai virus have been described by Kohler and Milstein (1975; 1976), and those using polyethylene glycol (PEG), such as 37% (v/v) PEG, by Gefter et al (1977). The use of electrically induced fusion methods also is appropriate (Goding pp. 71-74, 1986).

[0213] Fusion procedures usually produce viable hybrids at low frequencies, about 1×10⁻⁶ to 1×10⁻⁸. However, this does not pose a problem, as the viable, fused hybrids are differentiated from the parental, unfused cells (particularly the unfused myeloma cells that would normally continue to divide indefinitely) by culturing in a selective medium. The selective medium is generally one that contains an agent that blocks the de novo synthesis of nucleotides in the tissue culture media. Exemplary and preferred agents are aminopterin, methotrexate, and azaserine. HAT medium, a growth medium containing hypoxanthine, aminopterin and thymidine, is well known in the art as a medium for selection of hybrid cells. Aminopterin and methotrexate block de novo synthesis of both purines and pyrimidines, whereas azaserine blocks only purine synthesis. Where aminopterin or methotrexate is used, the media is supplemented with hypoxanthine and thymidine as a source of nucleotides (HAT medium). Where azaserine is used, the media is supplemented with hypoxanthine.

[0214] The preferred selection medium is HAT. Only cells capable of operating nucleotide salvage pathways are able to survive in HAT medium. The myeloma cells are defective in key enzymes of the salvage pathway, e.g., hypoxanthine phosphoribosyl transferase (HPRT), and they cannot survive. The B cells can operate this pathway, but they have a limited life span in culture and generally die within about two weeks. Therefore, the only cells that can survive in the selective media are those hybrids formed from myeloma and B cells.

[0215] This culturing provides a population of hybridomas from which specific hybridomas are selected. Typically, selection of hybridomas is performed by culturing the cells by single-clone dilution in microtiter plates, followed by testing the individual clonal supernatants (after about two to three weeks) for the desired reactivity. The assay should be sensitive, simple and rapid, such as radioimmunoassays, enzyme immunoassays, cytotoxicity assays, plaque assays, dot immunobinding assays, and the like.

[0216] The selected hybridomas then would be serially diluted and cloned into individual antibody-producing cell lines, which clones can then be propagated indefinitely to provide mAbs. The cell lines may be exploited for mAb production in two basic ways. First, a sample of the hybridoma can be injected (often into the peritoneal cavity) into a histocompatible animal of the type that was used to provide the somatic and myeloma cells for the original fusion (e.g., a syngeneic mouse). Optionally, the animals are primed with a hydrocarbon, especially oils such as pristane (tetramethylpentadecane) prior to injection. The injected animal develops tumors secreting the specific monoclonal antibody produced by the fused cell hybrid. The body fluids of the animal, such as serum or ascites fluid, can then be tapped to provide mAbs in high concentration. Second, the individual cell lines could be cultured in vitro, where the mAbs are naturally secreted into the culture medium from which they can be readily obtained in high concentrations.

[0217] mAbs produced by either means may be further purified, if desired, using filtration, centrifugation and various chromatographic methods such as HPLC or affinity chromatography. Fragments of the monoclonal antibodies of the invention can be obtained from the monoclonal antibodies so produced by methods which include digestion with enzymes, such as pepsin or papain, and/or by cleavage of disulfide bonds by chemical reduction. Alternatively, monoclonal antibody fragments encompassed by the present invention can be synthesized using an automated peptide synthesizer.

[0218] It also is contemplated that a molecular cloning approach may be used to generate monoclonals. For this, combinatorial immunoglobulin phagemid libraries are prepared from RNA isolated from the spleen of the immunized animal, and phagemids expressing appropriate antibodies are selected by panning using cells expressing the antigen and control cells. The advantages of this approach over conventional hybridoma techniques are that approximately 10⁴ times as many antibodies can be produced and screened in a single round, and that new specificities are generated by H and L chain combination which further increases the chance of finding appropriate antibodies.

[0219] Alternatively, monoclonal antibody fragments encompassed by the present invention can be synthesized using an automated peptide synthesizer, or by expression of full-length gene or of gene fragments in, for example, E. coli.

[0220] F. Pharmaceutical Compositions

[0221] Aqueous compositions of the present invention comprise an effective amount of a purified Chlamydia polynucleotide and/or a purified Chlamydia a protein, polypeptide, peptide, epitopic core region, and the like, dissolved and/or dispersed in a pharmaceutically acceptable carrier and/or aqueous medium. Aqueous compositions of gene therapy vectors expressing any of the foregoing are also contemplated.

[0222] The phrases “pharmaceutically and/or pharmacologically acceptable” refer to molecular entities and/or compositions that do not produce an adverse, allergic and/or other untoward reaction when administered to an animal.

[0223] As used herein, “pharmaceutically acceptable carrier” includes any and/or all solvents, dispersion media, coatings, antibacterial and/or antifungal agents, isotonic and/or absorption delaying agents and the like. The use of such media and/or agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media and/or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions. For animal and more particularly human administration, preparations should meet sterility, pyrogenicity, general safety and/or purity standards as required by FDA Office of Biologics standards.

[0224] The biological material should be extensively dialyzed to remove undesired small molecular weight molecules and/or lyophilized for more ready formulation into a desired vehicle, where appropriate. The active compounds may generally be formulated for parenteral administration, e.g., formulated for injection via the intravenous, intramuscular, sub-cutaneous, intralesional, and/or even intraperitoneal routes, or formulated for oral or inhaled delivery. The preparation of an aqueous compositions that contain an effective amount of purified Chlamydia polynucleotide or polypeptide agent as an active component and/or ingredient will be known to those of skill in the art in light of the present disclosure. Typically, such compositions can be prepared as injectables, either as liquid solutions and/or suspensions; solid forms suitable for using to prepare solutions and/or suspensions upon the addition of a liquid prior to injection can also be prepared; and/or the preparations can also be emulsified.

[0225] The pharmaceutical forms suitable for injectable use include sterile aqueous solutions and/or dispersions; formulations including sesame oil, peanut oil and/or aqueous propylene glycol; and/or sterile powders for the extemporaneous preparation of sterile injectable solutions and/or dispersions. In all cases the form must be sterile and/or must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and/or storage and/or must be preserved against the contaminating action of microorganisms, such as bacteria and/or fungi.

[0226] Solutions of the active compounds as free base and/or pharmacologically acceptable salts can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and/or mixtures thereof and/or in oils. Under ordinary conditions of storage and/or use, these preparations contain a preservative to prevent the growth of microorganisms.

[0227] A Chlamydia polynucleotide or polypeptide of the present invention can be formulated into a composition in a neutral and/or salt form. Pharmaceutically acceptable salts, include the acid addition salts (formed with the free amino groups of the protein) and/or which are formed with inorganic acids such as, for example, hydrochloric and/or phosphoric acids, and/or such organic acids as acetic, oxalic, tartaric, mandelic, and/or the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, and/or ferric hydroxides, and/or such organic bases as isopropylamine, trimethylamine, histidine, procaine and/or the like. In terms of using peptide therapeutics as active ingredients, the technology of U.S. Pat. Nos. 4,608,251; 4,601,903; 4,599,231; 4,599,230; 4,596,792; and/or 4,578,770, each incorporated herein by reference, may be used.

[0228] The carrier can also be a solvent and/or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and/or liquid polyethylene glycol, and/or the like), suitable mixtures thereof, and/or vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and/or by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and/or antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and/or the like. In many cases, it will be preferable to include isotonic agents, for example, sugars and/or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and/or gelatin.

[0229] Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and/or the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and/or freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. The preparation of more, and/or highly, concentrated solutions for direct injection is also contemplated, where the use of DMSO as solvent is envisioned to result in extremely rapid penetration, delivering high concentrations of the active agents to a small tumor area.

[0230] Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and/or in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described above, but drug release capsules and/or the like can also be employed.

[0231] For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and/or the liquid diluent first rendered isotonic with sufficient saline and/or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and/or intraperitoneal administration. In this connection, sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage could be dissolved in 1 ml of isotonic NaCl solution and/or either added to 1000 ml of hypodermoclysis fluid and/or injected at the proposed site of infusion, (see for example, “Remington's Pharmaceutical Sciences” 15th Edition, pages 1035-1038 and/or 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.

[0232] A Chlamydia polynucleotide or protein-derived peptides and/or agents may be formulated within a therapeutic mixture to comprise about 0.0001 to 1.0 milligrams, and/or about 0.001 to 0.1 milligrams, and/or about 0.1 to 1.0 and/or even about 10 milligrams per dose and/or so. Multiple doses can also be administered.

[0233] In addition to the compounds formulated for parenteral administration, such as intravenous and/or intramuscular injection, other pharmaceutically acceptable forms include, e.g., tablets and/or other solids for oral administration; liposomal formulations; time release capsules; and/or any other form currently used, including cremes.

[0234] One may also use nasal solutions and/or sprays, aerosols and/or inhalants in the present invention. Nasal solutions are usually aqueous solutions designed to be administered to the nasal passages in drops and/or sprays. Nasal solutions are prepared so that they are similar in many respects to nasal secretions, so that normal ciliary action is maintained. Thus, the aqueous nasal solutions usually are isotonic and/or slightly buffered to maintain a pH of 5.5 to 6.5. In addition, antimicrobial preservatives, similar to those used in ophthalmic preparations, and/or appropriate drug stabilizers, if required, may be included in the formulation. Various commercial nasal preparations are known and/or include, for example, antibiotics and/or antihistamines and/or are used for asthma prophylaxis.

[0235] Additional formulations which are suitable for other modes of administration include vaginal suppositories and/or pessaries. A rectal pessary and/or suppository may also be used. Suppositories are solid dosage forms of various weights and/or shapes, usually medicated, for insertion into the rectum, vagina and/or the urethra. After insertion, suppositories soften, melt and/or dissolve in the cavity fluids. In general, for suppositories, traditional binders and/or carriers may include, for example, polyalkylene glycols and/or triglycerides; such suppositories may be formed from mixtures containing the active ingredient in the range of 0.5% to 10%, preferably 1%-2%.

[0236] Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and/or the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations and/or powders. In certain defined embodiments, oral pharmaceutical compositions will comprise an inert diluent and/or assimilable edible carrier, and/or they may be enclosed in hard and/or soft shell gelatin capsule, and/or they may be compressed into tablets, and/or they may be incorporated directly with the food of the diet. For oral therapeutic administration, the active compounds may be incorporated with excipients and/or used in the form of ingestible tablets, buccal tables, troches, capsules, elixirs, suspensions, syrups, wafers, and/or the like. Such compositions and/or preparations should contain at least 0.1% of active compound. The percentage of the compositions and/or preparations may, of course, be varied and/or may conveniently be between about 2 to about 75% of the weight of the unit, and/or preferably between 25-60%. The amount of active compounds in such therapeutically useful compositions is such that a suitable dosage will be obtained.

[0237] The tablets, troches, pills, capsules and/or the like may also contain the following: a binder, as gum tragacanth, acacia, cornstarch, and/or gelatin; excipients, such as dicalcium phosphate; a disintegrating agent, such as corn starch, potato starch, alginic acid and/or the like; a lubricant, such as magnesium stearate; and/or a sweetening agent, such as sucrose, lactose and/or saccharin may be added and/or a flavoring agent, such as peppermint, oil of wintergreen, and/or cherry flavoring. When the dosage unit form is a capsule, it may contain, in addition to materials of the above type, a liquid carrier. Various other materials may be present as coatings and/or to otherwise modify the physical form of the dosage unit. For instance, tablets, pills, and/or capsules may be coated with shellac, sugar and/or both. A syrup of elixir may contain the active compounds sucrose as a sweetening agent methyl and/or propylparabens as preservatives, a dye and/or flavoring, such as cherry and/or orange flavor.

[0238] G. Kits

[0239] Therapeutic kits of the present invention are kits comprising a Chlamydia polynucleotide or polypeptide or an antibody to the polypeptide. Such kits will generally contain, in a suitable container, a pharmaceutically acceptable formulation of a Chlamydia polynucleotide or polypeptide, or an antibody to the polypeptide, or vector expressing any of the foregoing in a pharmaceutically acceptable formulation. The kit may have a single container, and/or it may have a distinct container for each compound.

[0240] When the components of the kit are provided in one and/or more liquid solutions, the liquid solution is an aqueous solution, with a sterile aqueous solution being particularly preferred. The Chlamydia polynucleotide or polypeptide, or antibody compositions may also be formulated into a syringeable composition. In which case, the container may itself be a syringe, pipette, and/or other such like apparatus, from which the formulation may be applied to an infected area of the body, injected into an animal, and/or even applied to and/or mixed with the other components of the kit.

[0241] However, the components of the kit may be provided as dried powder(s). When reagents and/or components are provided as a dry powder, the powder can be reconstituted by the addition of a suitable solvent. It is envisioned that the solvent may also be provided in another container.

[0242] The container will generally include at least one vial, test tube, flask, bottle, syringe and/or other container, into which the Chlamydia polynucleotide or polypeptide, or antibody formulation are placed, preferably, suitably allocated. The kits may also comprise a second container for containing a sterile, pharmaceutically acceptable buffer and/or other diluent.

[0243] The kits of the present invention will also typically include a means for containing the vials in close confinement for commercial sale, such as, e.g., injection and/or blow-molded plastic containers into which the desired vials are retained.

[0244] Irrespective of the number and/or type of containers, the kits of the invention may also comprise, and/or be packaged with, an instrument for assisting with the injection/administration and/or placement of the ultimate Chlamydia polynucleotide or polypeptide,or an antibody to the polypeptide within the body of an animal. Such an instrument may be a syringe, pipette, forceps, and/or any such medically approved delivery vehicle.

H. EXAMPLES

[0245] The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Example 1

[0246] Exemplary ELI Protocol

[0247] The following sections outline general methodology that one might use to prepare, screen and utilize ELI according to the present invention. Of course the following methods are merely general guidelines and should not limit one of skill in the art from modifying the present invention to accomplish a desired goal using ELI.

[0248] 1. Library Construction

[0249] The present invention provides expression library constructs of genus Chlamydia psittacii. An expression library of Chlamydia psittaci can be produced by first physically shearing the genomic DNA of Chlamydia psittaci (e.g., Chlamydia psittaci strain B577) and size-selecting fragments of 300-800 base pairs. The protocol used by the present inventors to produce a Chlamydia psittaci library is similar to that described in Sykes and Johnston (1999). Adaptors were added and the DNA fragments ligated into a genetic immunization vector (FIG. 2) designed to link fragments to the mouse ubiquitin gene. However, the fragments can be blunt-end cloned.

[0250] This vector is known to enhance MHC class I-restricted immune responses (Sykes and Johnston, 1999), while sterilizing immunity against Chlamydia is thought to be MHC class II-dependent (Morrison et al., 1995). However, any genetic immunization procedure, by the mechanism of intracellular expression of the inserted genes, will target towards class I antigen presentation. Nevertheless, both MHC class I- and class II-restricted immune responses to the expressed antigens are well documented (Barry et al., 1995; Sykes and Johnston, 1999). The inventors observed, for instance, pronounced delayed-type hypersensitivity responses, mediated by MEC II-restricted CD4⁺ Th1 cells, against protective Chlamydia psittaci B577 antigens, which were expressed from the ubiquitin fusion vector. In addition to the fact that MUC II-restricted immunity is generated by the ubiquitin fusion vector, MHC I-restricted immunity appears to mediate protection in the early phase of chlamydial infection (Morrison et al., 1995; Rottenberg et al., 1999). This duality of the cellular immune response generated by the ubiquitin fusion vector might explain the efficacy of this vector for genetic immunization against intracellular bacteria.

[0251] A library of approximately 82,000 individual members was created and tested as 27 sub-libraries each with 2,400-3,400 plasmid clones. The average insert frequency was approximately 67% and the average insert size was 660 base pairs. Nitrocellulose replica filters were made of each original colony plating of a sub-library pool for subsequent retrieval of positive clones. This generated a library with approximately six-fold expression-equivalent redundancy. One expression equivalent is defined as the number of in-frame fragments necessary to completely represent all authentic open reading frames. Since the genome size of Chlamydia psittaci is approximately 1×10⁶ base pairs and only one-sixth of the actual open-reading frames will be cloned in the right orientation and frame, it requires at least six genomic equivalents to encode one expression equivalent. Each sub-library was propagated on plates and harvested to prepare DNA. DNA representing each sub-library was used for genetic immunization of mice in the following section.

[0252] 2. Vaccination and Challenge

[0253] For the first round of testing, outbred, 6-week old, female NIH-Swiss Webster mice were inoculated with the purified DNA of each sub-library using both intra-muscular (i.m.) and epidermal injection. The epidermal injection was effected with a gene gun (Sanford et al., 1991). Each mouse was given 50 μg DNA i.m. and 5 μg DNA by gene gun. It has been argued that the gene gun immunization favors a Th2 and the i.m. injection a Th1 type response (Feltquate et al., 1997), therefore both types of injection were given to each group. In the first round of testing, the prime inoculation was followed by a boost 9 weeks later, before intranasal challenge with 3×10⁶ inclusion forming units (IFU) of Chlamydia psittaci strain B577 13 weeks after prime inoculation. The animals were sacrificed 12 days after the challenge, and lungs were weighed.

[0254] 3. Library Deconvolution

[0255] The basic scheme for handling the reduction of the libraries is depicted in FIG. 3. Fourteen groups out of the first round looked promising, so the individual clones from these groups were picked and grown in 96 well microtiter plates. This gave approximately 40,000 wells in microtiter plates, therefore about 40,000 clones. The second round was reduced using a two dimensional array format. As depicted in FIG. 3, the DNA was prepared from colonies pooled from rows and columns of the array. The rationale was that if a row and column conferred protection, the colonies at the intersection would be responsible. This scheme is premised on largely additive effects of the protective clones. This 24×24 array yielded pools of ˜1,700 clones with each intercession having ˜96 clones. Currently the inventors deconvolute the second round with a 3-dimensional array.

[0256] Since the lung weight was highly variable in the outbred NIH-Swiss mice with variable MHC background, the inventors decided to use inbred BALB/c mice in subsequent rounds. The 48 DNA pools for round two were i.m. injected into BALB/c mice at 50 μg DNA/animal, and the animals were boosted at seven weeks by both gene gun inoculation and i.m. injection. The mice were given a higher Chlamydia psittaci challenge, 1.6×10⁶ IFU Chlamydia psittaci B577, at approximately 12 weeks, again to further differentiate the groups. Animals were sacrificed and results evaluated as in round one.

[0257] In the fourth round, the animals received two boosts rather than one, and the challenge inoculum was increased to 3×10⁶ IFU Chlamydia psittaci B577 to increase the selectivity of protection scoring. Furthermore, because too much DNA may lead to a decrease in cellular immune response, the amount of each individual clone was reduced by half, with the difference made up with pUC118 DNA, so each mouse received a total 50 μg DNA for i.m. immunization, but only 25 μg of the specific clone. The inventors also decreased the gene gun DNA in the same manner: 1.25 μg/ear of the specific clone and 1.25 μg pUC118. Mice were boosted i.m. at both four and nine weeks after prime inoculation, and were challenged. The results of this final round are depicted in FIG. 5.

[0258] 4. Analysis of Sequences

[0259] The clones conferring protection were re-sequenced and then compared by BLAST search to Genbank and particularly to the recently completed Chlamydia pneumoniae (Kalman et al., 1999) genome sequences (FIG. 6). Of the 14 single genes identified in this study, ten are internal fragments and three contain the C-terminus of the protein. Of the five most protective clones, one was from a putative outer membrane protein and one was from a cell surface protein. The other three were from cytosolic proteins.

[0260] Four of the 14 clones have sequence similarity to a class of proteins known as putative outer membrane proteins (POMPs) in Chlamydia psittaci and Chlamydia pneumoniae. Many of the “putative” outer membrane proteins are known to be localized to the outer membrane and to be highly immunogenic (Longbottom et al., 1996; Tan et al., 1990).

[0261] 5. Mixing Experiment

[0262] The two dimensional approach used to find protective gene fragments assumes that the protection is due to a single highly protective gene within a pool. To verify that such genes would be found, 25 ng (i.e. 1/2000) of either of the two most protective genes was added to a pool that scored negative (pool 6 round 1). As depicted in FIG. 7, spiking with either clone converted the negative library to a positive.

Example 2

[0263] Materials and Methods

[0264] Library construction. Chlamydia psittaci strain B577 (ATCC VR-656) was grown in BGMK cells and elementary bodies (EB) were purified by renograff gradient centrifugation as described (Huang et al., 1999). Genomic DNA was isolated from EB by proteinase K and RNase digestion followed by cetyl-trimethyl ammonium bromide (Kaltenbock et al., 1997).

[0265] Genomic DNA was physically sheared using a nebulizer (Glas Col, Terra Haute, Ind.), then size fractioned on a 1.5% TBE agarose gel. Agarose with fragments between 300-700 base pairs was excised and the DNA was electroeluted. Adaptors (top strand 5′: GATCTGGATCCCGAT (SEQ ID NO.2) ATCGGGCTCCA (SEQ ID NO.3) onto the fragments, then the fragments were cloned into pCMVi-UBs at the Bgl II site (See FIG. 6 and Sykes and Johnston, 1999 for more details). The ligations were transformed into DH 5 alpha electrocompetent cells and plated onto 150 mm diameter YT-Ampicillin (75 μg/mL final concentration) plates. The resulting plates had between 2400-3400 individual clones per plate. After the plates were incubated overnight at 37° C., the colonies from were lifted using nitrocellulose filters soaked in L-Broth with 8% DMSO, and these filters were stored at −80° C. The original agar plates were then incubated at 37° C. for an additional six hours. Ten mL of L Broth was added to each plate, the E. coli was scraped into 150 mL of L-Broth and grown at 37° C. for 30 minutes. Ampicillin was then added to a final concentration of 50 μg/mL, and the cultures were grown overnight at 37° C. Cells were pelleted and the DNA was purified using Qiagen tip 500 columns.

[0266] Inoculation of DNA. Round One: DNA from the pools was injected into 6-week old female NIH-Swiss mice. All mice received 50 μg total DNA by i.m. injections, evenly distributed between the quadriceps and tibialis anterior muscles. Eighteen of the groups also received gene gun inoculations (wand), with 2.5 μg DNA inoculated into each ear. The animals were boosted once at nine weeks in the same manner as the primary inoculation—all mice received i.m. injections, but only the same 18 groups received gene gun injections—then intranasally challenged with 5.5×10⁵ IFU of Chlamydia psittaci strain B577 at 13 weeks. The mice were sacrificed 11 days after the challenge, and lungs were weighed.

[0267] Round Two: Nitrocellulose filters from the positive pools were placed on L-Broth Bio-Assay plates supplemented with 75 μg/mL ampicillin and 2% agar. The filters were incubated on the plates for approximately 15 minutes, then the nitrocellulose was discarded. The colonies were grown at 30° C. for 12 hours. The majority of the colonies were picked into 96 well microtiter plates containing HYT media (1.6% Bacto-tryptone, 1.0% Bacto-yeast extract, 85.5 mM NaCl, 36 mM K₂HPO₄, 13.2 mM KH₂PO₄, 1.7 mM Sodium citrate, 0.4 mM MgSO4, 6.8 mM ammonium sulfate, 4.4% wt/vol glycerol) supplemented with 75 μg/mL ampicillin, using a Hybaid colony picker; the plates were then visually inspected and the remainder of the colonies were hand-picked. The microtiter plates were designated by their original pool number and by the order in which they were picked. Hence, plate 5.10 was from original pool 5 and was the tenth plate picked. The colonies were subdivided into groups as is indicated in FIG. 2. All of the microtiter plates comprising a pool were stamped onto on L-Broth Bio-Assay plates supplemented with 75 μg/mL ampicillin and were grown overnight at 37° C. The cells from these plates were harvested by adding L-Broth to the plates and scraping off the cells. The cells were pelleted by centrifugation then resuspended in Qiagen buffer P1. The remainder of the DNA prep proceeded according to manufacture's instructions.

[0268] These 48 DNA pools were i.m. injected into 6-week old BALB/c mice at 50 μg DNA/animal. For the initial inoculation, the mice did not receive gene gun inoculations. At seven weeks, the mice were boosted with 50 μg DNA/animal. In addition to the i.m. injections, the first 31 groups received gene gun (Rumsey-Loomis) inoculations at 2.5 μg DNA/ear; however, the gene gun failed at group 32, and the last 17 groups received only i.m. injections. The mice were given a higher challenge, 1.6×10⁶ IFU Chlamydia psittaci B577, at 12 weeks. Animals were sacrificed as in round one.

[0269] Round Three: Colonies from the microtiter plates that were judged to be positive were arrayed as in FIG. 2. For each pool, new microtiter plates with HYT media supplemented with 75 μg/mL ampicillin were constructed from all of the colonies which comprise the. Colonies were grown and DNA prepared as in round two.

[0270] The mice received both gene gun (wand) and i.m. inoculations at the dosage indicated above. At six weeks, the mice were boosted with 50 μg DNA/animal, but only by i.m. injections. The challenge schedule was the same as in Round Two.

[0271] Round Four: E. coli from wells at either full by full protection or full by partial protection was streaked out onto YT-plates supplemented with 75 μg/mL ampicillin. Six colonies from each of the plates were tested by PCR colony screening, using the primers FS-UB 5′: CCGCACCCTCTCTGATTAC (SEQ ID No: 4) CTGGAGTGGCAACTTCC. (SEQ ID NO. 5) Colonies with different sizes, hence different inserts, were sequenced using ABI Big Dye terminator and the FS-UB primer. Samples were purified on G-50 spin columns, and run on an ABI 377 Sequencer. The generated sequences were analyzed for open reading frames using a program designed by Simon Raynor, Ph.D.

Example 3

[0272] Vaccination and Challenge

[0273] It was established that the weight increase of the infected lung over the lung weight of naïve, uninfected controls (˜120 mg) correlated strongly with disease intensity. Maximum disease in this model resulted in approximately 250% lung weight increase, while further lung weight increases were lethal. The lung disease on day 12 after inoculation was characterized by areas of gross lung tissue consolidation and the presence of mononuclear interstitial infiltrates in consolidated tissue. Chlamydial inclusions were observed by immunohistochemistry in many macrophages, but rarely in other cells. Controls for complete protection were established by low level intranasal infection of naïve mice with 3×10⁴IFU of Chlamydia psittaci strain B577 4 weeks prior to challenge. These mice were completely protected from disease after challenge infection and had lung weight increases of 10-30% compared to naïve animals. Lungs of completely protected mice did not show gross lung lesions, and pathohistological examination revealed no interstitial infiltrates, but prominent peribronchiolar lymphocytic cuffs, interpreted as sign of protective immune stimulation. The chlamydial lung burden on day 11 after challenge was typically 1-3×10⁶ IFU per 100 mg lung tissue in protected, and 2-6×10⁶ IFU per 100 mg lung in diseased animals. Since the lowest chlamydial burden was, however, not consistently associated with lowest disease, the inventors used the disease-dependent parameter lung weight rather than chlamydial burden as readout for evaluation of protection. The lung weights were transformed to relative protection scores in a linear equation that assumed the high average lung weight of the severely ill, naïve, challenged mice as 0 and that of fully protected controls as 1 (FIG. 4).

[0274] Example 4

[0275] Deconvolution of the Libraries

[0276] Since the lung weight was highly variable in the outbred NIH-Swiss mice with variable MHC background, the inventors decided to use inbred BALB/c mice in subsequent rounds. The 48 DNA pools for round two were i.m. injected into BALB/c mice at 50 μg DNA/animal, and the animals were boosted at seven weeks by both gene gun inoculation and i.m. injection. The mice were given a higher Chlamydia psittaci challenge, 1.6×10⁶ IFU Chlamydia psittaci B577, at approximately 12 weeks, again to further differentiate the groups. Animals were sacrificed and results evaluated as in round one.

[0277] The results of the Round two challenge are depicted in FIG. 4. Of the 48 groups from round two, 15 were judged to be positive, giving a total of 3936 wells. These wells were again arrayed as in round two, but the array had 112 colonies per column and 156 per row with 4-5 colonies per intersection (See FIG. 3). The mice received both gene gun and i.m. injections at the dosage indicated above. At six weeks, the mice were boosted. Both the challenge and the sacrifice were performed as in Round two.

[0278] The positive 46 colonies from the intersection wells from Round three were sequenced, and those clones with open reading frames greater than 50 amino acids long were prepared individually and shot into mice as single genes and as a pool. Fourteen clones met these criteria. The disease scoring on each pool in rounds 1-3 are depicted in FIG. 4.

[0279] In the fourth round, the animals received two boosts rather than one, and the challenge inoculum was increased to 3×10⁶ IFU Chlamydia psittaci B577 to increase the selectivity of protection scoring. Furthermore, because too much DNA may lead to a decrease in cellular immune response, the amount of each individual clone was reduced by half but made up the difference with pUC118 DNA, and each mouse received a total 50 μg DNA for i.m. immunization, but only 25 μg of the specific clone. The inventors also decreased the gene gun DNA in the same manner: 1.25 μg/ear of the specific clone and 1.25 μg pUC118. Mice were boosted i.m. at both four and nine weeks after prime inoculation, and were challenged. The results of this final round are depicted in FIG. 5.

Example 5

[0280] Comparison of Clones

[0281] Based on the hypothesis that sequences from genes conferring a high level of protection might be selected more than once in the ELI process, the clones were compared against each other for overlaps. Interestingly, one of the clones, CP4 #10, did overlap with another gene, CP4 #11. The gene from which these two clones arise had been partially sequenced (Longbottom et al., 1998).

[0282] Two of the genes, CP4 #5 and CP4 #9, had an overlapping region, but they were fused to ubiqutin in opposite orientations. CP4 #5, is composed of two different Chlamydia psittaci DNA fragments, fused in opposite orientations. The first gene is fused to ubiqutin in the correct orientation and the correct reading frame. Interestingly, the second gene, which is in the opposite orientation to the ubiqutin gene, has an overlapping sequence to CP4 #5. It is doubtful that the protein from the second gene is produced in the mouse.

Example 6

[0283] Analysis of Sequences

[0284] The clones conferring protection were re-sequenced and then compared by BLAST search to Genbank and particularly to the recently completed Chlamydia pneumoniae (Kalman et al., 1999) genome sequences (FIG. 6). The full-length Chlamydia psittaci genes were next isolated and sequences. Upon analysis, all nucleic acid sequences, except #4, #10, #11, and #12, were previously undisclosed in any context. Further, only protions of the sequences encoding #10 and #11 were previously disclosed.

[0285] Since most protective genes would not have been predicted by any bioinformatics or information-based approach, it is likely that one will need to apply an unbiased, global approach, such as ELI to define vaccine candidates.

[0286] Table 2, lists a comparison of the Chlamydia psittaci genes with homologues from Chlamydia trachomatis and Chlamydia pneumoniae. TABLE 2 Identity/ Identity/ Chlamydia ps Chlamydia trachomatis Similarity Chlamydia pneumoniae Similarity CP4 #1 DNA Pol III Gamma and Tau 62/73 DNA Pol III Gamma and Tau 66/76 CP4 #2 Glu-tRNA Gln Amido- 49/70 Glu-tRNA Gln Amido- 48/63 transferase (C subunit) transferase (C subunit) CP4 #3 Glu-tRNA Gln Amido- 71/85 Glu-tRNA Gln Amido- 71/84 transferase (A subunit) transferase (A subunit) CP4 #4 OMP 90A Outer Membrane Protein 5 30/45 Outer Membrane Protein G Family 40/54 Outer Membrane Protein G/I Family 28/46 CP4 #5 Transglycolase/transpeptidase 67/80 Transglycolase/transpeptidase 67/77 CP4 #6 Protein Translocase 80/89 Protein Translocase 84/92 CP4 #7 Outer Membrane Lipoprotein 60/79 CP4 #8 Oligopeptidase 60/75 Oligopeptidase 61/74 CP4 #9 Hypothetical protein 62/76 Hypothetical protein 62/77 CP4 #10 Outer Membrane Protein 4 27/42 Outer Membrane Protein G Family 33/51 CP4 #11 Outer Membrane Protein 4 27/42 Outer Membrane Protein G Family 33/51 CP4 #12 OMP 98 kDa Outer Membrane Protein 5 30/43 Outer membrane Protein G Family 44/58 CP4 #13 Protein Translocase 80/89 Protein Translocase 84/92 CP4 #14 Succinate Dehydrogenase 60/76 Succinate Dehydrogenase 61/77

[0287] Table 3 lists all of the cloned fragments, their corresponding full length nucleotide sequences, and the amino acid sequences encoded by both the fragments and the full length sequences. Table 2 further describes the fragments. TABLE 3 SEQUENCE LISTING INDEX SEQ ID NO CP4_NO Description SEQ ID NO: 6 CP4 #1 (fragment) homolog to Chlamydia pneumoniae DNA Pol III Gamma and Tau subunits (dnaX2 gene) SEQ ID NO: 7 CP4 #1 Polypeptide translation corresponding to SEQ ID NO. 6, homolog to Chlamydia pneumoniae DNA Pol III Gamma and Tau subunits (dnaX2 gene) SEQ ID NO: 8 CP4 #1 (full length) homolog to Chlamydia pneumoniae DNA Pol III Gamma and Tau subunits (dnaX2 gene) SEQ ID NO: 9 CP4 #1 Polypeptide translation corresponding to SEQ ID NO. 8, homolog to Chlamydia pneumoniae DNA Pol III Gamma and Tau subunits (dnaX2 gene) SEQ ID NO: 10 CP4 #2 (fragment) homolog to Chlamydia pneumoniae Glu- tRNA Gln Amido-transferase (C subunit) (gatC gene) SEQ ID NO: 11 CP4 #2 Polypeptide translation corresponding to SEQ ID NO. 10, homolog to Chlamydia pneumoniae Glu-tRNA Gln Amido-transferase (C subunit) (gatC gene) SEQ ID NO: 12 CP4 #2 (full length) homolog to Chlamydia pneumoniae Glu- tRNA Gln Amido-transferase (C subunit) (gatC gene) SEQ ID NO: 13 CP4 #2 Polypeptide translation corresponding to SEQ ID NO. 12, homolog to Chlamydia pneumoniae Glu-tRNA Gln Amido-transferase (C subunit) (gatC gene) SEQ ID NO: 14 CP4 #3 (fragment) homolog to Chlamydia pneumoniae Glu- tRNA Gln Amido-transferase (A subunit) (gatA gene) SEQ ID NO: 15 CP4 #3 Polypeptide translation corresponding to SEQ ID NO. 14, homolog to Chlamydia pneumoniae Glu-tRNA Gln Amido-transferase (A subunit) (gatA gene) SEQ ID NO: 16 CP4 #3 (full length) homolog to Chlamydia pneumoniae Glu- tRNA Gln Amido-transferase (A subunit) (gatA gene) SEQ ID NO: 17 CP4 #3 Polypeptide translation corresponding to SEQ ID NO. 16, homolog to Chlamydia pneumoniae Glu-tRNA Gln Amido-transferase (A subunit) (gatA gene) SEQ ID NO: 18 CP4 #3 (full length) homolog to Chlamydia pneumoniae Glu- tRNA Gln Amido-transferase (B subunit) (gatB gene) SEQ ID NO: 19 CP4 #3 Polypeptide translation corresponding to SEQ ID NO. 18, homolog to Chlamydia pneumoniae Glu-Trna Gln Amido-transferase (B subunit) (gatB gene) SEQ ID NO: 20 CP4 #4 (fragment) Chlamydia psittaci 90 kDa outer membrane protein (OMP90A gene) (Previously sequenced by Longbottom, et al); homolog to Chlamydia pneumoniae Outer Membrane Protein G/I (pmp 9) and Outer Membrane Protein G (pmp 5) SEQ ID NO: 21 CP4 #4 Polypeptide translation corresponding to SEQ ID NO. 20, Chlamydia psittaci 90 kDa outer membrane protein (OMP90A gene); homolog to Chlamydia pneumoniae Outer Membrane Protein G/I (pmp 9) and Outer Membrane Protein G (pmp 5) SEQ ID NO: 22 CP4 #4 (full length) Chlamydia psittaci 90 kDa outer membrane protein (OMP90A gene) (Previously sequenced by Longbottom, et al); homolog to Chlamydia pneumoniae Outer Membrane Protein G/I (pmp 9) and Outer Membrane Protein G (pmp 5) SEQ ID NO: 23 CP4 #4 Polypeptide translation corresponding to SEQ ID NO. 22, Chlamydia psittaci 90 kDa outer membrane protein (OMP90A gene); homolog to Chlamydia pneumoniae Outer Membrane Protein G/I (pmp 9) and Outer Membrane Protein G (pmp 5) SEQ ID NO: 24 CP4 #5 (fragment) homolog to Chlamydia pneumoniae transglycolase/transpeptidase (pbp3 gene) SEQ ID NO: 25 CP4#5 Polypeptide translation corresponding to SEQ ID NO. 24, homolog to Chlamydia pneumoniae transglycolase/transpeptidase(pbp3 gene) SEQ ID NO: 26 CP4 #5 (full length) homolog to Chlamydia pneumoniae transglycolase/transpeptidase (pbp3 gene) SEQ ID NO: 27 CP4 #5 Polypeptide translation corresponding to SEQ ID NO. 26, homolog to Chlamydia pneumoniae transglycolase/transpeptidase (pbp3 gene) SEQ ID NO: 28 CP4 #6 (fragment) homolog to Chlamydia pneumoniae Protein Translocase (secA2 gene) SEQ ID NO: 29 CP4 #6 Polypeptide translation corresponding to SEQ ID NO. 28, homolog to Chlamydia pneumoniae Protein Translocase (secA2 gene) SEQ ID NO: 30 CP4 #13 (fragment) homolog to Chlamydia pneumoniae Protein Translocase (secA2 gene) SEQ ID NO: 31 CP4 #13 Polypeptide translation corresponding to SEQ ID NO. 30, homolog to Chlamydia pneumoniae Protein Translocase (secA2 gene) SEQ ID NO: 32 CP4 #6 & 13 (full length) homolog to Chlamydia pneumoniae Protein Translocase (secA2 gene) SEQ ID NO: 33 CP4 #6 & 13 Polypeptide translation corresponding to SEQ ID NO. 32, homolog to Chlamydia pneumoniae Protein Translocase (secA2 gene) SEQ ID NO: 34 CP4 #7 (fragment) homolog to Chlamydia pneumoniae Outer Membrane Lipoprotein (Cpn 0278) SEQ ID NO: 35 CP4 #7 Polypeptide translation corresponding to SEQ ID NO. 34, homolog to Chlamydia pneumoniae Outer Membrane Lipoprotein (Cpn 0278 gene) SEQ ID NO: 36 CP4 #7 (full length) homolog to Chlamydia pneumoniae Outer Membrane Lipoprotein (Cpn 0278) SEQ ID NO: 37 CP4 #7 Polypeptide translation corresponding to SEQ ID NO. 36, homolog to Chlamydia pneumoniae Outer Membrane Lipoprotein (Cpn 0278 gene) SEQ ID NO: 38 CP4 #8 (fragment) homolog to Chlamydia pneumoniae Oligopeptidase (pepF gene) SEQ ID NO: 39 CP4 #8 Polypeptide translation corresponding to SEQ ID NO. 38, homolog to Chlamydia pneumoniae Oligopeptidase (pepF gene) SEQ ID NO: 40 CP4 #8 (full length) homolog to Chlamydia pneumoniae Oligopeptidase (pepF gene) SEQ ID NO: 41 CP4 #8 Polypeptide translation corresponding to SEQ ID NO. 40, homolog to Chlamydia pneumoniae Oligopeptidase (pepF gene) SEQ ID NO: 42 CP4 #9 (fragment) homolog to Chlamydia pneumoniae gene of unknown function, co-translationaly coupled to Yop N Flagellar-Type ATPase (Cpn 0708 gene) SEQ ID NO: 43 CP4 #9 Polypeptide translation corresponding to SEQ ID NO. 42, homolog to Chlamydia pneumoniae gene of unknown function, co-translationally coupled to Yop N Flagellar- Type ATPase (Cpn 0708 gene) SEQ ID NO: 44 CP4 #9 (full length) homolog to Chlamydia pneumoniae gene of unknown function, co-translationally coupled to Yop N Flagellar-Type ATPase (Cpn 0708 gene) SEQ ID NO: 45 CP4 #9 Polypeptide translation corresponding to SEQ ID NO. 44, homolog to Chlamydia pneumoniae gene of unknown function, co-translationally coupled to Yop N Flagellar- Type ATPase (Cpn 0708 gene) SEQ ID NO: 46 CP4 #9 (full length) homolog to Chlamydia pneumoniae Yop N Flagellar-Type ATPase (yscN gene) SEQ ID NO: 47 CP4 #9 Polypeptide translation corresponding to SEQ ID NO. 46, homolog to Chlamydia pneumoniae Yop N Flagellar- Type ATPase (yscN gene) SEQ ID NO: 48 CP4 #10 (fragment) homolog to Chlamydia pneumoniae outer membrane protein G (pmp 2 gene) (Nucleotides 1-423 were previously sequenced by Longbottom et al.) SEQ ID NO: 49 CP4 #10 Polypeptide translation corresponding to SEQ ID NO. 48, homolog to Chlamydia pneumoniae outer membrane protein G (pmp 2 gene) SEQ ID NO: 50 CP4 #11 (fragment) homolog to Chlamydia pneumoniae outer membrane protein G (pmp 2 gene) (Nucleotides 1-301 were previously sequenced by Longbottom et al.) SEQ ID NO: 51 CP4 #11 Polypeptide translation corresponding to SEQ ID NO. 50, homolog to Chlamydia pneumoniae outer membrane protein G (pmp 2 gene) SEQ ID NO: 52 CP4 #10 & (full length) homolog to Chlamydia pneumoniae outer 11 membrane protein G (pmp 2 gene). This gene immediately follows the OMP90A gene on Chlamydia psittaci, and nucleotides 1-502 were published by Longbottom et al., although they did not report this as a gene. SEQ ID NO: 53 CP4 #10 & Polypeptide translation corresponding to SEQ ID NO. 52, 11 homolog to Chlamydia pneumoniae outer membrane protein G (pmp 2 gene). SEQ ID NO: 54 CP4 #12 (fragment) Chlamydia psittaci 98 kDa outer membrane protein (POMP gene) (Previously sequenced by Longbottom, et al) SEQ ID NO: 55 CP4 #12 Polypeptide translation corresponding to SEQ ID NO. 54, Chlamydia psittaci 98 kDa outer membrane protein (POMP gene) SEQ ID NO: 56 CP4 #12 (full length) Chlamydia psittaci 98 kDa outer membrane protein (POMP gene) (Previously sequenced by Longbottom et al.) SEQ ID NO: 57 CP4 #12 Polypeptide translation corresponding to SEQ ID NO. 56, Chlamydia psittaci 98 kDa outer membrane protein (POMP gene) SEQ ID NO: 58 CP4 #14 (fragment) homolog to Chlamydia pneumoniae Succinate Dehydrogenase (sdhC) SEQ ID NO: 59 CP4 #14 Polypeptide translation corresponding to SEQ ID NO. 58, homolog to Chlamydia pneumoniae Succinate Dehydrogenase (sdhC gene) SEQ ID NO: 60 CP4 #14 (full length) homolog to Chlamydia pneumoniae Succinate Dehydrogenase (sdhC) SEQ ID NO: 61 CP4 #14 Polypeptide translation corresponding to SEQ ID NO. 60, homolog to Chlamydia pneumoniae Succinate Dehydrogenase (sdhC gene)

[0288] Of the 14 single genes identified in this study, ten are internal fragments and three contain the C-terminus of the protein. Of the five most protective clones (CP4 #1-5), one was from a putative outer membrane protein (CP4 #4) and one was from a cell surface protein (CP4 #5). The other three were from cytosolic proteins, with CP4 #2 and CP4 #3 deriving independently from genes encoding a particular amidotransferase complex.

[0289] Four of the 14 clones have sequence similarity to a class of proteins known as putative outer membrane proteins (POMPs) in Chlamydia psittaci and Chlamydia pneumoniae (CP4 #4, CP4 #10, CP4 #11 and CP4 #12). Many of the “putative” outer membrane proteins are known to be localized to the outer membrane and to be highly immunogenic (Longbottom et al., 1996; Tan et al., 1990). The clone designated CP4 #4 is an in-frame fragment of POMP90A (Longbottom et al., 1998) and CP4 #12 is an in-frame fragment of a 98 kDa POMP which has been completely sequenced (Accession U72499). The clones CP4 #10 and CP4 #11 immediately follow CP4 #4 in the genome and have sequence similarity to POMPs in Chlamydia psittaci, Chlamydia trachomatis and Chlamydia pneumoniae. As stated earlier, the clone CP4 #10 overlaps the CP4 #11 clone. Of these clones only CP4 #4 confers significant protection in isolation so clearly the criteria of being an outer membrane protein is not sufficient to predict a protective vaccine.

[0290] Example 7

[0291] Mixing Experiment

[0292] The two dimensional approach used to find protective gene fragments assumes that the protection is due to a single highly protective gene within a pool. To verify that such genes would be found, 25 ng (i.e. 1/2000) of either CP4 #4 or CP4 #11 was added to a pool that scored negative (pool 6 round 1). As depicted in FIG. 7, spiking with either clone converted the negative library to a positive. Of note is that CP4 #11 did not confer protection when tested individually, however, it does protect in combination.

[0293] The fact that a CP4 #4 positive library confers protection validates the sensitivity of the system. The fact that a CP4 #11 positive library protects implies that CP4 #11 con be a useful component of a vaccine, but that it may depend upon having other antigens present. A likely explanation is that CP4 #11 is a good vaccine antigen, but requires immunological help.

Example 8

[0294] Vaccination in Cattle

[0295] An important question is whether the genes identified in this manner in a mouse model are clinically relevant. Of course, this concern is not peculiar to genetic vaccines or ELI, but any system that uses models to identify vaccine candidates. In this case the clinically relevant situation is protection of cattle. In a preliminary experiment, the inventors evaluated the pool of 14 individual clones in the original host in a fertility challenge model. All fourteen clones were used as the individual test data on each clone in mice was not available by the time it was necessary to initiate the cow trial. TABLE 4 Chlamydia psittaci Vaccine in Cows Percent Not Pregnant Pregnant Pregnant Not Challenged 75 3 1 Challenged, 0 0 4 Not Vaccinated EB Vaccine 25 1 3 Genetic Vaccine 33 2 4 (14 gene pool)

[0296]Chlamydia psittaci is normally introduced by the fecal-oral and respiratory routes in cattle, and disseminates to other tissues including reproductive organs. Chlamydia psittaci infection of the uterine mucosa reduces fertility, the basis of the economic interest in a Chlamydia psittaci vaccine. Four groups of heifers were used. One group was the naïve unchallenged control, another the naïve, challenged control, a third received the same pool of fourteen gene fragments that were tested in mice, and the fourth group was vaccinated with an experimental, inactivated vaccine of elementary bodies (EB) and also challenged. This EB vaccine had shown great promise in field trials but is too expensive to produce. After a prime and one boost, the heifers were estrus synchronized by prostaglandin injection, were in heat 2-3 days later, and were artificially inseminated, simultaneously receiving an intracervical chlamydial challenge of 3×10⁷ inclusion forming units. The heifers were palpated for pregnancy at six weeks after insemination. This challenge was very high in order to maximize the difference between positive and negative control animals. This was necessary because only a small number of cows could be justified for this high-risk experiment.

[0297] Although the animal numbers are small, the results are quite encouraging. As is seen in Table 4, three out of four animals became pregnant in the positive control (non-challenged) group, 0/4 in the negative control (non-vaccinated, challenged) group, 2/6 in the genetic immunization group, and 1/4 in the elementary body vaccine group. The genetic vaccine of the pooled genes performed at least as well as the EB vaccine. Also relative to the inventor's interest in therapeutic vaccines, these cows were not sterile with respect to Chlamydia psittaci at the time of the prime inoculation. The vaccination was in the face of previous exposure and low level Chlamydia psittaci infection, as determined by the high titers of preinoculation antichlamydial antibodies, and occasional positivity of Chlamydia omp1 PCRs from vaginal scrapings.

[0298] The next phase in developing a cow vaccine will be to experimentally verify the effectiveness of particular groups of the protective genes and then convert the codon usage of the Chlamydia psittaci genes to that of a mammal. This should increase the expression of the antigen in cows and increase the effectiveness of the vaccine. The inventors will test different combinations of those genes which have been found to be individually protective, as well as combinations with CP4 #11. Both the original fragments and their full-length versions can be tested, both as nucleic acid segments and proteins. Once the combinations have been verified in mice or other small mammals, those combinations showing the most promise will be tested in cows. After immunization, the cows will be challenged with Chlamydia psittaci, either by direct challenge at insemination or infection by herd-mates. Direct challenge at insemination is a very severe and unnatural form of challenge. Therefore, even if protection is not demonstrated in the wake of such challenge, this does not necessarily mean that no protection has been conferred upon the cows.

Example 9

[0299] Fertility at 42 Days Post Breeding in Heifers Vaccinated with the Pool of the 5 Best Mouse-protective Genes of Chlamydia psittaci

[0300] Because it is known that bacterial genes are not expressed efficiently in mammalian cells, the five most protective genes were chemically resynthesized to give an optimal mammalian codon bias. In addition, the full-length genes corresponding to the fragments isolated in the screen were used.

[0301] One group of five heifers was vaccinated with this pool. Another group of six heifers was vaccinated with an Alum-Quil A based vaccine containing per dose 100 μg each of the affinity-purified protein fragments expressed in E. coli from these genes. The control group of twelve heifers was vaccinated with a plasmid expressing an unrelated bacterial gene. Six weeks after the initial immunization all groups received booster vaccinations. Eight weeks later all heifers, including a cohort of 27 non-vaccinated heifers, were estrus-synchronized by prostaglandin injection. After coming into heat two to three days later, the non-vaccinated cohort heifers were infected with an intrauterine chlamydial inoculum of 10⁸ IFUs C. psittaci B577. The function of this group was to shed chlamydiae, and thus to challenge through natural infection routes the vaccinated animals at the time of breeding. Eleven days later, the vaccinated animals were re-synchronized, and inseminated at estrus. The heifers were rectally palpated for pregnancy determination at six weeks after insemination.

[0302] The Genetic Vaccine group was vaccinated with DNA comprised of the pool of 5 full length, mammalianized genes, the Protein Vaccine group with the 5 full-length proteins, and the control group with DNA of an unrelated gene from Salmonella typhimurium. During the 3-week period prior to C. psittaci infection, heifers of all groups, including the non-vaccinated challenge cohort, shed low levels of C. psittaci (0.5±0.2 genomes/swab) as determined by qPCR of weekly collected vaginal cytobrush swabs. To challenge the vaccinated animals via natural transmission at the time of breeding, a cohort of 27 non-vaccinated animals was intracervically infected with C. psittaci. Eleven days later, all vaccinated groups were estrus-synchronized and inseminated. During the 4 weeks following the infection, the infected cohort animals shed high levels of chlamydiae (3826±2052 genomes per swab), and then returned to low baseline shedding (24.2±10.9 genomes per swab) for the remaining 5-week observation period. All vaccinated heifers were exposed to the natural challenge infection, as evident in their 7-fold increased post-breeding shedding of chlamydiae (3.6±1.2 genomes/swab; p<0.05) compared to pre-breeding shedding of all heifers. No difference in chlamydial shedding before or after breeding was found between the C. psittaci vaccinated and the control vaccinated groups. TABLE 5 Fertility in cows vaccinated with a pooi of the 5 best mouse-protective Chlamydia psittaci genes. Group Percent Pregnant Pregnant Not Pregnant Control Group 50 6 6 Genetic Vaccine 80 4 1 Protein Vaccine 83 5 1

[0303] As is seen in Table 5, six out of twelve animals (50% fertility) became pregnant in the control group, 4/5 or (80% fertility in the genetic vaccine group, and five out of six (83% fertility) in the protein vaccine group. Thus, 9/11 animals in both vaccine groups were pregnant. The genetic vaccine of the pooled genes performed as well as the protein vaccine. These fertility data correspond very well with typical data of bovine herds with and without fertility problems. When both vaccine groups combined are compared to the controls, the 1-tailed Fisher's exact test indicates with a p=0.122 that vaccination is effective to improve Chlamydia-induced reduction of fertility. The odds ratio for improvement of fertility by vaccination is 4.5 (0.67-30.23, 95% confidence interval). These data are important in view of the fact that all heifers in the experiment had been previously exposed to chlamydiae and experienced low-level herd infection with C. psittaci, as determined by positive C. psittaci B577 MOMP-peptide ELISA and sporadic detection by quantitative PCR of low levels of C. psittaci in pre-challenge vaginal cytobrush swabs.

Example 10

[0304] Creation and Testing of Vaccines Using Chlamydia psittaci Nucleic Acid and Amino Acid Sequences to Protect Non-bovine Species

[0305] The Chlamydia psittaci sequences and antigens disclosed in this application are envisioned to be used in vaccines for Chlamydia psittaci in commercially important animals such as dairy cattle. Field trials in cattle are being conducted, as described above. However, these Chlamydia psittaci sequences may be used to create vaccines for other species as well, including other species of Chlamydia and other bacterial pathogens.

[0306] For example, one may use the information gained concerning Chlamydia psittaci to identify a sequence in another bacterial pathogen that had substantial homology to the Chlamydia psittaci sequences. In many cases, this homology would be expected to be more than 30% amino acid sequence identity or similarity and could be for only part of a protein, e.gg 30 amino acids, in the other species. The gene encoding such identity/similarity may be isolated and tested as a vaccine candidate in the appropriate model system either as a protein or nucleic acid. Alternatively, the Chlamydia psittaci homologs may be tested directly in an animal species of interest since having so few genes to screen (10 or less) and given that the genes had been demonstrated to be protective in another species the probability of success would be high. Alternatively, proteins or peptides corresponding to the homologs to the Chlamydia psittaci genes may be used to assay in animals or humans for immune responses in people or animals infected with the relevant pathogen. If such immune responses are detected, particularly if they correlated with protection, then the genes, proteins or peptides corresponding to the homologs may be tested directly in animals or humans as vaccines.

Example 11

[0307] Creation and Testing of Commercial Vaccines Using Chlamydia psittaci Nucleic Acid and Amino Acid Sequences

[0308] The genes identified and claimed as vaccine candidates can be developed into commercial vaccines in the following manner. The genes identified can be converted to optimized mammalian expression sequences by changing the codons. This is a straightforward procedure, which can be easily do by one of skill in the art, and has been done for the Chlamydia psittaci sequences. The genes can then be tested in the relevant host, for example, cattle, for the relevant protection, for example, fertility. Genetic immunization affords a simple method to test vaccine candidate for efficacy and this form of delivery has been used in a wide variety of animals including humans. Alternatively, the genes may be transferred to another vector, for example, a vaccinia vector, to be tested in the relevant host in this form. Alternatively, the corresponding protein, with or without adjuvants may be tested. These tests may be done on a relatively small number of animals. Once conducted, a decision can be made as to how many of the protective antigens to include in a larger test. Only a subset may be chosen based on the economics of production. A large field trial may be conducted using the formulation arrived at. Based on the results of the field trial, possibly done more than once at different locations, a commercial vaccine would go into production.

Example 12

[0309] Creation and Testing of Vaccines Against Other Pathogens Using Chlamydia Nucleic Acid and Amino Acid Sequences

[0310] Since Chlamydia pneumonia has a similar pathobiology as Chlamydia psittaci, the inventors take advantage of the screening already accomplished on the Chlamydia psittaci genome to test Chlamydia pneumoniae for homologs corresponding to the ones from Chlamydia psittaci as vaccine candidates. Those of ordinary skill may expect that, as one moved evolutionarily away from Chlamydia psittaci, the likelihood that the homologs would protect would presumably decline. However, researchers would be likely to test the homologs identified from even disparate species for protective ability in regard to relevant diseases, as this could reduce the search of a genome for vaccine candidates ˜200-1,000 fold. Once the homologs have been identified and isolated, they may be tested in the appropriate animal model system for efficacy as a vaccine. For example, the Chlamydia pneumonia homologs as genes or proteins can be tested in a mouse pneumonia model or in a mouse or rabbit atherosclerosis model.

[0311] In an example, showing the applicability of the use of homology to determine protective antigens in differing genera, it has been shown that hsp65, the Mycobacterium tuberculosis homolog of the Chlamydia pneumonia hsp60 gene, is protective against Mycobacterium tuberculosis, just as hsp60 is protective against Chlamydia pneumonia. This validates that homologous genes from two different pathogens can result in protective genetic vaccines against those pathogens. Therefore, there is a strong impetus to use the Chlamydia gene sequences that have been disclosed as protective herein, and other such sequences that may be determined by the methods disclosed herein, to search for protective sequences of other species.

[0312] To prove this concept, full length gene of Chlamydia pneumonia homolog of Chlamydia psittacii underwent PCR and the animals were challenged with Chlamydia pneumonia. The gene that conferred protection against Chlamydia psittaci gave the best protection against Chlamydia pneumonia. As demonstrated in FIG. 8 and Table 6, the genes of Chlamydia pneumonia dnaX2 (SEQ. ID NO 62), gatA (SEQ. ID NO 64); pbp3 (SEQ. ID NO 66); and the unknown gene 0278 (SEQ. ID NO 68), and their respective amino acid sequences (SEQ. ID NO 63, SEQ. ID NO 65, SEQ. ID NO 67, and SEQ. ID NO 69), conferred protection against Chlamydia pneumonia. TABLE 6 Protection (log of colonies in lung) against Chlamydia pneumoniae Name of gene Protection Vaccinated Ctr 53 **C pn. dna2 5.4 C.pn. gatC 7.3 **C. pn gatA 6.5 C.pn. Pmp5 7.4 C.pn Pmp9 76 **C.pn. Pbp3 6.4 C.pn. SecA 72 **C.pn. Unk.0278 6.7 C.pn pepF 7.2 C.pn. 0708 7.2 C.pn Pmp2 70 pool, 5 best C. psittaci 70 Irrelev. Vacc. 69

[0313] The above study indicates that, once one of ordinary skill has access to the Chlamydia sequences disclosed in this specification, or to additional sequences determined to be protective using any of the methods disclosed in this specification, it is easy to run a computer-based search of relevant genetic databases in order to determine homologous sequences in other pathogens. For example, these searches can be run in the BLAST database in GenBank.

[0314] Once a sequence which is homologous to a protective sequence is determined, it is possible to obtain the homologous sequence using any of a number of methods known to those of skill. For example, it is easy to PCR amplify the pathogen homolog genes from genomic DNA and clone the genes into an appropriate genetic immunization vector, such as those used for ELI. These homolog genes can then be tested in an animal model appropriate for the pathogen for which protection is sought, to determine whether homologs of the Chlamydia genes will protect a host from challenge with that pathogen.

[0315] For example, the dnaX2 gene from Chlamydia psittaci is homologous to the dnaX2 gene from Helicobacter pylori. Therefore, one can will amplify the dnaX2 gene from Helicobacter pylor genomic DNA and clone it into a genetic immunization vector. The clone could then be tested for protection by inoculating animals with the Helicobacter pylor dnaX2 clone, then challenging the inoculated animals with Helicobacter pylor bacteria.

[0316] Of course, it is possible for one of ordinary skill to use the Chlamydia genes that are disclosed as protective herein, or determined to be protective using the methods disclosed herein, to obtain protective sequences from a first non-Chlamydia organism, then to use the protective sequences from the non-Chlamydia organism to search for homologous sequences in a second non-Chlamydia or Chlamydia organism. So long as a protective Chlamydia sequence is used as the starting point for determining at least one homology in such a chain of searches and testing, such methods are within the scope of this invention.

[0317] All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

[0318] References

[0319] The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.

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1 69 1 127 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 1 ctgcacctgg tccttcgcct gagaggtgca gatcttggat cctaagtaag taagcttgca 60 tgcctgcagg tcgactctag gtgactaata tctagaggat cgatcccggg tggcatccct 120 gtgaccc 127 2 15 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 2 gatctggatc ccgat 15 3 11 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 3 atcgggctcc a 11 4 19 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 4 ccgcaccctc tctgattac 19 5 17 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 5 ctggagtggc aacttcc 17 6 449 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 6 gaatgtattc gcacgcaaaa atacgctgaa gctttgcttc ctgtcacgac agcgatcaat 60 tctggagtcg cgcctatcac cttcctccat gacctcactg ttttttatcg cgatgtactg 120 ctaaacaaag atcagggaaa ttctcctcta tcggccatcg ccatgcacta ttccagtgaa 180 tgtttattag aaatcattga tttccttggt gaagcggcca aacatctaca acaaactatt 240 tttgaaaaaa catttttaga aacagtcatc atccatctta ttcggatatg ccaacgtccc 300 tctttagaaa ctctgttttc tcaactgaaa acatccacgt ttgatacagt gagaaacgta 360 ccccagcagc aagaaccctc gaaaccgagt atacaacctg aaaaacacta tcaagatcag 420 agtttcttaa cttcaccttc tcccacgcc 449 7 149 PRT Chlamydia psittaci 7 Glu Cys Ile Arg Thr Gln Lys Tyr Ala Glu Ala Leu Leu Pro Val Thr 1 5 10 15 Thr Ala Ile Asn Ser Gly Val Ala Pro Ile Thr Phe Leu His Asp Leu 20 25 30 Thr Val Phe Tyr Arg Asp Val Leu Leu Asn Lys Asp Gln Gly Asn Ser 35 40 45 Pro Leu Ser Ala Ile Ala Met His Tyr Ser Ser Glu Cys Leu Leu Glu 50 55 60 Ile Ile Asp Phe Leu Gly Glu Ala Ala Lys His Leu Gln Gln Thr Ile 65 70 75 80 Phe Glu Lys Thr Phe Leu Glu Thr Val Ile Ile His Leu Ile Arg Ile 85 90 95 Cys Gln Arg Pro Ser Leu Glu Thr Leu Phe Ser Gln Leu Lys Thr Ser 100 105 110 Thr Phe Asp Thr Val Arg Asn Val Pro Gln Gln Gln Glu Pro Ser Lys 115 120 125 Pro Ser Ile Gln Pro Glu Lys His Tyr Gln Asp Gln Ser Phe Leu Thr 130 135 140 Ser Pro Ser Pro Thr 145 8 1332 DNA Chlamydia psittaci 8 atgacatcag caacatacca agtttcttct agaaaatacc gccctcaaac atttgccgaa 60 atgctggggc aagatgccgt ggtcactgtt ttaaaaaatg ctttgcagtt tcaacgtgtc 120 gcgcatgcgt atttattttc agggattcgc ggaacaggaa aaacaacttt agcaagaatc 180 tttgcaaaag ccttaaactg taaagagctg actcctgaac atgaaccatg caaccagtgt 240 tgtgtttgta aagaaatctc ttcaggaacc tccttagacg tgatcgaaat cgatggtgcc 300 tcgcaccgag gtattgaaga tatccgtcaa atcaatgaaa ccgtgctctt tactcctgcc 360 aaatcacaat ataaaatcta tatcatagat gaagtccata tgctgactaa ggaggcgttt 420 aattccttac tcaaaacttt agaagagcct ccgagccatg taaaattctt cttagcgact 480 acagaaaatt ataaaatacc cagcaccatt ttaagtcgtt gtcaaaaaat gcacctaaag 540 agaattcctg agacaatgat tgtagataag ctagcatcca tatctcaagc aggtgggata 600 gaaacctctc gagaagctct tcttcctatt gctagagcag cacagggaag cttacgcgat 660 gctgaatctc tttatgatta tgtcataggg ttattcccta catctttatc cccagagttg 720 gttgcagacg cattaggttt attatctcaa gacaccttag ctacattatc agaatgtatt 780 cgcacgcaaa aatacgctga agctttgctt cctgtcacga cagcgatcaa ttctggagtc 840 gcgcctatca ccttcctcca tgacctcact gttttttatc gcgatgtact gctaaacaaa 900 gatcagggaa attctcctct atcggccatc gccatgcact attccagtga atgtttatta 960 gaaatcattg atttccttgg tgaagcggcc aaacatctac aacaaactat ttttgaaaaa 1020 acatttttag aaacagtcat catccatctt attcggatat gccaacgtcc ctctttagaa 1080 actctgtttt ctcaactgaa aacatccacg tttgatacag tgagaaacgt accccagcag 1140 caagaaccct cgaaaccgag tatacaacct gaaaaacact atcaagatca gagtttctta 1200 acttcacctt ctcccacgcc aaaagttcag catcaaaaag aagcttcccc ttctttagtg 1260 ggatcagcta ctatagatac gcttttacaa tttgctgttg ttgagttttc cggaatttta 1320 accaaggagt aa 1332 9 443 PRT Chlamydia psittaci 9 Met Thr Ser Ala Thr Tyr Gln Val Ser Ser Arg Lys Tyr Arg Pro Gln 1 5 10 15 Thr Phe Ala Glu Met Leu Gly Gln Asp Ala Val Val Thr Val Leu Lys 20 25 30 Asn Ala Leu Gln Phe Gln Arg Val Ala His Ala Tyr Leu Phe Ser Gly 35 40 45 Ile Arg Gly Thr Gly Lys Thr Thr Leu Ala Arg Ile Phe Ala Lys Ala 50 55 60 Leu Asn Cys Lys Glu Leu Thr Pro Glu His Glu Pro Cys Asn Gln Cys 65 70 75 80 Cys Val Cys Lys Glu Ile Ser Ser Gly Thr Ser Leu Asp Val Ile Glu 85 90 95 Ile Asp Gly Ala Ser His Arg Gly Ile Glu Asp Ile Arg Gln Ile Asn 100 105 110 Glu Thr Val Leu Phe Thr Pro Ala Lys Ser Gln Tyr Lys Ile Tyr Ile 115 120 125 Ile Asp Glu Val His Met Leu Thr Lys Glu Ala Phe Asn Ser Leu Leu 130 135 140 Lys Thr Leu Glu Glu Pro Pro Ser His Val Lys Phe Phe Leu Ala Thr 145 150 155 160 Thr Glu Asn Tyr Lys Ile Pro Ser Thr Ile Leu Ser Arg Cys Gln Lys 165 170 175 Met His Leu Lys Arg Ile Pro Glu Thr Met Ile Val Asp Lys Leu Ala 180 185 190 Ser Ile Ser Gln Ala Gly Gly Ile Glu Thr Ser Arg Glu Ala Leu Leu 195 200 205 Pro Ile Ala Arg Ala Ala Gln Gly Ser Leu Arg Asp Ala Glu Ser Leu 210 215 220 Tyr Asp Tyr Val Ile Gly Leu Phe Pro Thr Ser Leu Ser Pro Glu Leu 225 230 235 240 Val Ala Asp Ala Leu Gly Leu Leu Ser Gln Asp Thr Leu Ala Thr Leu 245 250 255 Ser Glu Cys Ile Arg Thr Gln Lys Tyr Ala Glu Ala Leu Leu Pro Val 260 265 270 Thr Thr Ala Ile Asn Ser Gly Val Ala Pro Ile Thr Phe Leu His Asp 275 280 285 Leu Thr Val Phe Tyr Arg Asp Val Leu Leu Asn Lys Asp Gln Gly Asn 290 295 300 Ser Pro Leu Ser Ala Ile Ala Met His Tyr Ser Ser Glu Cys Leu Leu 305 310 315 320 Glu Ile Ile Asp Phe Leu Gly Glu Ala Ala Lys His Leu Gln Gln Thr 325 330 335 Ile Phe Glu Lys Thr Phe Leu Glu Thr Val Ile Ile His Leu Ile Arg 340 345 350 Ile Cys Gln Arg Pro Ser Leu Glu Thr Leu Phe Ser Gln Leu Lys Thr 355 360 365 Ser Thr Phe Asp Thr Val Arg Asn Val Pro Gln Gln Gln Glu Pro Ser 370 375 380 Lys Pro Ser Ile Gln Pro Glu Lys His Tyr Gln Asp Gln Ser Phe Leu 385 390 395 400 Thr Ser Pro Ser Pro Thr Pro Lys Val Gln His Gln Lys Glu Ala Ser 405 410 415 Pro Ser Leu Val Gly Ser Ala Thr Ile Asp Thr Leu Leu Gln Phe Ala 420 425 430 Val Val Glu Phe Ser Gly Ile Leu Thr Lys Glu 435 440 10 123 DNA Chlamydia psittaci 10 gagtttattc aagagtatga aagttcttta aatgaagtca ttaaaactat ggcagcatcc 60 atcgctatgg atgtaaccga cgtggttatt gaggttggtt tatcccatgt gatcagtccc 120 gaa 123 11 41 PRT Chlamydia psittaci 11 Glu Phe Ile Gln Glu Tyr Glu Ser Ser Leu Asn Glu Val Ile Lys Thr 1 5 10 15 Met Ala Ala Ser Ile Ala Met Asp Val Thr Asp Val Val Ile Glu Val 20 25 30 Gly Leu Ser His Val Ile Ser Pro Glu 35 40 12 303 DNA Chlamydia psittaci 12 atgacacaac cctatgtaac tagagaagac attatacttc tggcgaagag ttcagctctg 60 gaattaagcg aagagtttat tcaagagtat gaaagttctt taaatgaagt cattaaaact 120 atggcagcat ccatcgctat ggatgtaacc gacgtggtta ttgaggttgg tttatcccat 180 gtgatcagtc ccgaagattt acgagaagat atcgttgcct caagtttctc tcgtgaggag 240 tttctaacta atgtccctga atccttaggg ggattagtaa aagtacccac agtcattaag 300 tag 303 13 100 PRT Chlamydia psittaci 13 Met Thr Gln Pro Tyr Val Thr Arg Glu Asp Ile Ile Leu Leu Ala Lys 1 5 10 15 Ser Ser Ala Leu Glu Leu Ser Glu Glu Phe Ile Gln Glu Tyr Glu Ser 20 25 30 Ser Leu Asn Glu Val Ile Lys Thr Met Ala Ala Ser Ile Ala Met Asp 35 40 45 Val Thr Asp Val Val Ile Glu Val Gly Leu Ser His Val Ile Ser Pro 50 55 60 Glu Asp Leu Arg Glu Asp Ile Val Ala Ser Ser Phe Ser Arg Glu Glu 65 70 75 80 Phe Leu Thr Asn Val Pro Glu Ser Leu Gly Gly Leu Val Lys Val Pro 85 90 95 Thr Val Ile Lys 100 14 514 DNA Chlamydia psittaci 14 gaaaagtgtg atgtgattgc gatgcctgta tgctcatgcc cagcattcgc cgatggcgaa 60 atccttgatc ctacctctct atatctccag gatatctata ccgtggctat gaatttagcc 120 tacctcccag ctatcgccgt tccttcaggg ttttctcgag aagggctgcc tctaggattc 180 caggtgattg gacaaaaggg taaagatcaa caggtgtgcc aggtaggcta tagcttccaa 240 gaacattcag gaattaagaa tttataccct aaaggatgta acaaacttgt tgatggagag 300 gtgaaataat gagcgacgtt tatgctgatt gggaatccgt cataggtctt gaagtccacg 360 tagaattaaa cacaaaatct aaattgttca gttgtgcacg caaccgtttt ggagacgaac 420 ctaatacaaa catctctcct gtatgcaccg gcatgccggg gtcactgcca gtactgaata 480 aagaagcagt gagaaaggct gttttatttg gttg 514 15 102 PRT Chlamydia psittaci 15 Glu Lys Cys Asp Val Ile Ala Met Pro Val Cys Ser Cys Pro Ala Phe 1 5 10 15 Ala Asp Gly Glu Ile Leu Asp Pro Thr Ser Leu Tyr Leu Gln Asp Ile 20 25 30 Tyr Thr Val Ala Met Asn Leu Ala Tyr Leu Pro Ala Ile Ala Val Pro 35 40 45 Ser Gly Phe Ser Arg Glu Gly Leu Pro Leu Gly Phe Gln Val Ile Gly 50 55 60 Gln Lys Gly Lys Asp Gln Gln Val Cys Gln Val Gly Tyr Ser Phe Gln 65 70 75 80 Glu His Ser Gly Ile Lys Asn Leu Tyr Pro Lys Gly Cys Asn Lys Leu 85 90 95 Val Asp Gly Glu Val Lys 100 16 1476 DNA Chlamydia psittaci 16 atgtatcaga agagtgcctt agagttaaga aatgccgtag tgagtggaga gtcttcagct 60 acagcaatag caaagtattt ttataataga ataaaaacag aagacaatca gataggagct 120 tttctttctc tttgtgaaga aagagcttat gagaaagcag ctatcataga tgcgaaagtg 180 gcgcgaggag aacctttggg gaaactcgca ggtgtcccca tcgggataaa agataatatt 240 catattcggg gtttgcgcac cacttgtgct tctaaaatgt tagaaaatta tatagcgcct 300 tttgatgcta cagtcgtcga acggatagaa gctgaagatg gggtcatttt aggcaaactc 360 aatatggatg agtttgctat gggatcgaca acgcagtatt ctgctttcca tcctacgaaa 420 aatccttggg gtttatcctg tgtgccagga ggatcttcag ggggatccgc cgccgcagtt 480 tctgcaagat tttgtcctat agcgttaggt tcggataccg gtggatctat acgtcagcca 540 gcagcatttt gtggagttgt ggggtttaag ccctcctatg gagccgtctc ccgttacggt 600 ttagtcgctt ttgggtcttc attagatcag ataggccctt taacaacagt tgtcgaagat 660 gtcgccttag ctatggatgt attcgcaggt aaggatgata gagatgcaac ttctcagaag 720 ttttttacag gatctttcca agaggccttg tctttagacg ttccgagttt gatcggcgtg 780 cctatgggat ttttagacgg tttacgtgat gatgttaaag agaatttctt tgcctcttta 840 agtattttgg aacgtcaggg tagccgcatt gttgaagtgg atcttaacat cttagatcac 900 gctgtctctg tttactacat tgtcgcttct gcagaagccg caacaaatct tgcaagattt 960 gatggtattc gttacggcta tcgttctcca gaagcgcata gtatagaaga tatttatacg 1020 atctcccgcg tacaaggctt cggtaaggaa gtcatgcgta ggattctttt aggtaactat 1080 gtgttatcca ctgagcgcca aaatgtctat tataagaaag gctccgcaat tcgagcaaaa 1140 atcattcaag cttttcaaaa agcttatgaa aagtgtgatg tgattgcgat gcctgtatgc 1200 tcatgcccag cattcgccga tggcgaaatc cttgatccta cctctctata tctccaggat 1260 atctataccg tggctatgaa tttagcctac ctcccagcta tcgccgttcc ttcagggttt 1320 tctcgagaag ggctgcctct aggattccag gtgattggac aaaagggtaa agatcaacag 1380 gtgtgccagg taggctatag cttccaagaa cattcaggaa ttaagaattt ataccctaaa 1440 ggatgtaaca aacttgttga tggagaggtg aaataa 1476 17 491 PRT Chlamydia psittaci 17 Met Tyr Gln Lys Ser Ala Leu Glu Leu Arg Asn Ala Val Val Ser Gly 1 5 10 15 Glu Ser Ser Ala Thr Ala Ile Ala Lys Tyr Phe Tyr Asn Arg Ile Lys 20 25 30 Thr Glu Asp Asn Gln Ile Gly Ala Phe Leu Ser Leu Cys Glu Glu Arg 35 40 45 Ala Tyr Glu Lys Ala Ala Ile Ile Asp Ala Lys Val Ala Arg Gly Glu 50 55 60 Pro Leu Gly Lys Leu Ala Gly Val Pro Ile Gly Ile Lys Asp Asn Ile 65 70 75 80 His Ile Arg Gly Leu Arg Thr Thr Cys Ala Ser Lys Met Leu Glu Asn 85 90 95 Tyr Ile Ala Pro Phe Asp Ala Thr Val Val Glu Arg Ile Glu Ala Glu 100 105 110 Asp Gly Val Ile Leu Gly Lys Leu Asn Met Asp Glu Phe Ala Met Gly 115 120 125 Ser Thr Thr Gln Tyr Ser Ala Phe His Pro Thr Lys Asn Pro Trp Gly 130 135 140 Leu Ser Cys Val Pro Gly Gly Ser Ser Gly Gly Ser Ala Ala Ala Val 145 150 155 160 Ser Ala Arg Phe Cys Pro Ile Ala Leu Gly Ser Asp Thr Gly Gly Ser 165 170 175 Ile Arg Gln Pro Ala Ala Phe Cys Gly Val Val Gly Phe Lys Pro Ser 180 185 190 Tyr Gly Ala Val Ser Arg Tyr Gly Leu Val Ala Phe Gly Ser Ser Leu 195 200 205 Asp Gln Ile Gly Pro Leu Thr Thr Val Val Glu Asp Val Ala Leu Ala 210 215 220 Met Asp Val Phe Ala Gly Lys Asp Asp Arg Asp Ala Thr Ser Gln Lys 225 230 235 240 Phe Phe Thr Gly Ser Phe Gln Glu Ala Leu Ser Leu Asp Val Pro Ser 245 250 255 Leu Ile Gly Val Pro Met Gly Phe Leu Asp Gly Leu Arg Asp Asp Val 260 265 270 Lys Glu Asn Phe Phe Ala Ser Leu Ser Ile Leu Glu Arg Gln Gly Ser 275 280 285 Arg Ile Val Glu Val Asp Leu Asn Ile Leu Asp His Ala Val Ser Val 290 295 300 Tyr Tyr Ile Val Ala Ser Ala Glu Ala Ala Thr Asn Leu Ala Arg Phe 305 310 315 320 Asp Gly Ile Arg Tyr Gly Tyr Arg Ser Pro Glu Ala His Ser Ile Glu 325 330 335 Asp Ile Tyr Thr Ile Ser Arg Val Gln Gly Phe Gly Lys Glu Val Met 340 345 350 Arg Arg Ile Leu Leu Gly Asn Tyr Val Leu Ser Thr Glu Arg Gln Asn 355 360 365 Val Tyr Tyr Lys Lys Gly Ser Ala Ile Arg Ala Lys Ile Ile Gln Ala 370 375 380 Phe Gln Lys Ala Tyr Glu Lys Cys Asp Val Ile Ala Met Pro Val Cys 385 390 395 400 Ser Cys Pro Ala Phe Ala Asp Gly Glu Ile Leu Asp Pro Thr Ser Leu 405 410 415 Tyr Leu Gln Asp Ile Tyr Thr Val Ala Met Asn Leu Ala Tyr Leu Pro 420 425 430 Ala Ile Ala Val Pro Ser Gly Phe Ser Arg Glu Gly Leu Pro Leu Gly 435 440 445 Phe Gln Val Ile Gly Gln Lys Gly Lys Asp Gln Gln Val Cys Gln Val 450 455 460 Gly Tyr Ser Phe Gln Glu His Ser Gly Ile Lys Asn Leu Tyr Pro Lys 465 470 475 480 Gly Cys Asn Lys Leu Val Asp Gly Glu Val Lys 485 490 18 1464 DNA Chlamydia psittaci 18 atgagcgacg tttatgctga ttgggaatcc gtcataggtc ttgaagtcca cgtagaatta 60 aacacaaaat ctaaattgtt cagttgtgca cgcaaccgtt ttggagacga acctaataca 120 aacatctctc ctgtatgcac cggcatgccg gggtcactgc cagtactgaa taaagaagca 180 gtgagaaagg ctgttttatt tggttgtgct gttgaaggcg aagtagcttt gctcagccgt 240 tttgatagaa agtcctattt ttatcccgat agcccaagga attttcaaat tacccaattc 300 gaacatccta ttgtgcgagg aggacatata aaagctatcg ttcacggtga ggaacgtcat 360 tttgaactgg ctcaagcgca tatcgaagat gatgccggta tgctaaaaca tttcggagaa 420 tttgctggag tagattataa ccgcgctggt gtacctttaa tagagattgt gtctaagccg 480 tgcatgtttt gtgctgatga tgctgttgct tatgccacag ctttggtatc cttattagac 540 tacataggca tttctgactg taatatggaa gaaggctcgg tacgctttga tgtaaacata 600 tccgtacgtc ctaaaggtag cgaagaacta cgcaataaag tagaaattaa aaatatgaac 660 tcctttgctt ttatggccca agctctagaa gccgagcgtt gtcgtcagat cgatgcatat 720 ttagacaatc caaatgcaga ccccaaaact gttattccag gagcgacata ccgttgggat 780 cctgaaaaga aaaaaacagt gttgatgcgt cttaaggaac gagctgaaga ttacaagtat 840 ttcatagagc ctgatctccc agtattgcaa ttaacagaag catatattga tgaaattcgt 900 catacgcttc ccgagctccc tttcaacaaa taccaaaggt atttgcacga atatgctctt 960 gccgaagaca tcgctgccat tttaattagc gataagcata gtgcgcactt ctttgaatta 1020 gccgctcagg aatgtaaaaa ctacagagcc ctttctaatt ggttaactgt tgagtttgcc 1080 ggacgttgta aactcaaggg taagaatctc gctttctcag gtatcctgcc cagtagtgta 1140 gctcagcttg tgaattttat tgatcaaggc gtgattaccg gaaagatcgc taaggatatc 1200 gcagacatga tgatggaatc tcctgaaaag agtcctgaga ctatcctcaa agaaaatcct 1260 gaaatgttgc ccatgacaga tgaaagtgcg ttggtggcga tcatttccga ggtgattacc 1320 gcaaatccgc agtctgtcgt agactacaaa agtggtaaga ccaaggcgtt aggattttta 1380 gttgggcaaa ttatgaaacg tacccagggc aaggcccctc caaatagggt aaatgaactt 1440 ttgcttgtgg aattaagtaa ataa 1464 19 487 PRT Chlamydia psittaci 19 Met Ser Asp Val Tyr Ala Asp Trp Glu Ser Val Ile Gly Leu Glu Val 1 5 10 15 His Val Glu Leu Asn Thr Lys Ser Lys Leu Phe Ser Cys Ala Arg Asn 20 25 30 Arg Phe Gly Asp Glu Pro Asn Thr Asn Ile Ser Pro Val Cys Thr Gly 35 40 45 Met Pro Gly Ser Leu Pro Val Leu Asn Lys Glu Ala Val Arg Lys Ala 50 55 60 Val Leu Phe Gly Cys Ala Val Glu Gly Glu Val Ala Leu Leu Ser Arg 65 70 75 80 Phe Asp Arg Lys Ser Tyr Phe Tyr Pro Asp Ser Pro Arg Asn Phe Gln 85 90 95 Ile Thr Gln Phe Glu His Pro Ile Val Arg Gly Gly His Ile Lys Ala 100 105 110 Ile Val His Gly Glu Glu Arg His Phe Glu Leu Ala Gln Ala His Ile 115 120 125 Glu Asp Asp Ala Gly Met Leu Lys His Phe Gly Glu Phe Ala Gly Val 130 135 140 Asp Tyr Asn Arg Ala Gly Val Pro Leu Ile Glu Ile Val Ser Lys Pro 145 150 155 160 Cys Met Phe Cys Ala Asp Asp Ala Val Ala Tyr Ala Thr Ala Leu Val 165 170 175 Ser Leu Leu Asp Tyr Ile Gly Ile Ser Asp Cys Asn Met Glu Glu Gly 180 185 190 Ser Val Arg Phe Asp Val Asn Ile Ser Val Arg Pro Lys Gly Ser Glu 195 200 205 Glu Leu Arg Asn Lys Val Glu Ile Lys Asn Met Asn Ser Phe Ala Phe 210 215 220 Met Ala Gln Ala Leu Glu Ala Glu Arg Cys Arg Gln Ile Asp Ala Tyr 225 230 235 240 Leu Asp Asn Pro Asn Ala Asp Pro Lys Thr Val Ile Pro Gly Ala Thr 245 250 255 Tyr Arg Trp Asp Pro Glu Lys Lys Lys Thr Val Leu Met Arg Leu Lys 260 265 270 Glu Arg Ala Glu Asp Tyr Lys Tyr Phe Ile Glu Pro Asp Leu Pro Val 275 280 285 Leu Gln Leu Thr Glu Ala Tyr Ile Asp Glu Ile Arg His Thr Leu Pro 290 295 300 Glu Leu Pro Phe Asn Lys Tyr Gln Arg Tyr Leu His Glu Tyr Ala Leu 305 310 315 320 Ala Glu Asp Ile Ala Ala Ile Leu Ile Ser Asp Lys His Ser Ala His 325 330 335 Phe Phe Glu Leu Ala Ala Gln Glu Cys Lys Asn Tyr Arg Ala Leu Ser 340 345 350 Asn Trp Leu Thr Val Glu Phe Ala Gly Arg Cys Lys Leu Lys Gly Lys 355 360 365 Asn Leu Ala Phe Ser Gly Ile Leu Pro Ser Ser Val Ala Gln Leu Val 370 375 380 Asn Phe Ile Asp Gln Gly Val Ile Thr Gly Lys Ile Ala Lys Asp Ile 385 390 395 400 Ala Asp Met Met Met Glu Ser Pro Glu Lys Ser Pro Glu Thr Ile Leu 405 410 415 Lys Glu Asn Pro Glu Met Leu Pro Met Thr Asp Glu Ser Ala Leu Val 420 425 430 Ala Ile Ile Ser Glu Val Ile Thr Ala Asn Pro Gln Ser Val Val Asp 435 440 445 Tyr Lys Ser Gly Lys Thr Lys Ala Leu Gly Phe Leu Val Gly Gln Ile 450 455 460 Met Lys Arg Thr Gln Gly Lys Ala Pro Pro Asn Arg Val Asn Glu Leu 465 470 475 480 Leu Leu Val Glu Leu Ser Lys 485 20 379 DNA Chlamydia psittaci 20 tatttagtgt cgaaaaacaa cgccaacatt tacgcaggtt ctctctatta tcagcatatc 60 tcctattgga gcgcttggca gaatctgcta caaaacacta tcggtgcaga agctccgtta 120 gtccttaacg cacagttaac ttattgtcat gcttcaaacg acatgaaaac caacatgacg 180 actacttacg ctcctcgtaa aacaacgtat gcagaaatca agggtgattg gggtaacgat 240 tgtttcggag tcgagcttgg tgcaactgtg cctatccaaa cagaatcttc tctcctattc 300 gatatgtact cacctttcct gaagtttcaa cttgtgcata cgcaccaaga tgactttaag 360 gaaaacaata gcgatcagg 379 21 126 PRT Chlamydia psittaci 21 Tyr Leu Val Ser Lys Asn Asn Ala Asn Ile Tyr Ala Gly Ser Leu Tyr 1 5 10 15 Tyr Gln His Ile Ser Tyr Trp Ser Ala Trp Gln Asn Leu Leu Gln Asn 20 25 30 Thr Ile Gly Ala Glu Ala Pro Leu Val Leu Asn Ala Gln Leu Thr Tyr 35 40 45 Cys His Ala Ser Asn Asp Met Lys Thr Asn Met Thr Thr Thr Tyr Ala 50 55 60 Pro Arg Lys Thr Thr Tyr Ala Glu Ile Lys Gly Asp Trp Gly Asn Asp 65 70 75 80 Cys Phe Gly Val Glu Leu Gly Ala Thr Val Pro Ile Gln Thr Glu Ser 85 90 95 Ser Leu Leu Phe Asp Met Tyr Ser Pro Phe Leu Lys Phe Gln Leu Val 100 105 110 His Thr His Gln Asp Asp Phe Lys Glu Asn Asn Ser Asp Gln 115 120 125 22 2520 DNA Chlamydia psittaci 22 atgaaacatc cagtctactg gttcttaata tcctcgagcc tatttgcctc gaattctttg 60 agcttcgcta acgacgctca aacagcctta actccctccg atagctataa tggaaatgtg 120 acctctgagg agttccaggt aaaagaaact tcatcaggaa caacgtatac ttgtgaaggc 180 aatgtgtgta tctcctttgc agggaaagat tcaggtctaa agaaaagttg tttctcagct 240 actgataacc ttaccttcct aggaaacggg tatactcttt gctttgataa tattactact 300 acagctagta accccggagc cattaatgtt caaggtcaag gaaaaacctt aggcatctca 360 ggattttctt tattttcatg tgcttattgt cctccaggca caactggtta cggagctata 420 cagactaaag gcaacacaac tttaaaagat aactctagtc ttgtcttcca taaaaactgc 480 tcaacagcag aaggtggggc tatccagtgt aaaggaagca gtgatgctga attaaaaata 540 gaaaataatc agaatctggt tttctcagaa aactcctcca cttcaaaagg cggggctatt 600 tatgctgata aactcaccat tgtctcaggt gggcctacat tattttctaa caactctgta 660 tccaacggtt catcccctaa aggcggagct attagcataa aagattcaag tggtgaatgt 720 agcctaaccg ctgatctcgg agatattacc ttcgatggga acaaaatcat caaaactagt 780 ggtggaagtt ctacagtaac aagaaattcc atagatctcg gcacagggaa atttacaaag 840 ctacgtgcta aagacggctt cggaattttc ttctatgacc ctattactgg gggaggatct 900 gatgaactaa acattaataa aaaagaaact gttgattata caggaaagat cgtcttctca 960 ggtgaaaaat tatccgatga agaaaaagca cgagcggaaa acctagcttc tactttcaac 1020 caacccatca cattatcagc aggatctctt gtacttaaag atggtgtatc tgtaaccgca 1080 aaacaagtaa cgcaggaagc gggatctacc gttgtcatgg atctagggac cacattacag 1140 acgccttctt caggtggaga aaccatcacc ctaactaatc tagatattaa catcgcctcg 1200 ttgggggggg gggggggtac ctctcctgct aaactcgcaa caaatacagc aagtcaagct 1260 ataactatta acgctgtcaa tctagtcgat gctgatggca atgcttatga agatcctatt 1320 cttgctacgt ctaaaccttt cacagcaata gtagctacaa ctaacgctag tacagtcaca 1380 cagcctacag ataatctaac aaattatgtc cctcctactc attacggtta ccaaggaaat 1440 tggacagtaa cttgggacac cgaaacagct acaaaaacag ccactctaac ttgggaacaa 1500 actggctact cccctaaccc agaacgtcaa ggacctttag tcccgaatac tctttggggt 1560 gcattctctg acctcagagc tatacaaaac ttaatggata ttagcgtcaa tggcgctgac 1620 taccatagag gtttttgggt atccggtcta gctaacttct tacacaaaag tggctctgat 1680 actaaacgca agttccgtca caatagcgcc ggatacgctt taggcgtcta cgcaaaaact 1740 ccttctgatg atattttcag tgcggctttc tgccaactct tcggaaagga caaagactat 1800 ttagtgtcga aaaacaacgc caacatttac gcaggttctc tctattatca gcatatctcc 1860 tattggagcg cttggcagaa tctgctacaa aacactatcg gtgcagaagc tccgttagtc 1920 cttaacgcac agttaactta ttgtcatgct tcaaacgaca tgaaaaccaa catgacgact 1980 acttacgctc ctcgtaaaac aacgtatgca gaaatcaagg gtgattgggg taacgattgt 2040 ttcggagtcg agcttggtgc aactgtgcct atccaaacag aatcttctct cctattcgat 2100 atgtactcac ctttcctgaa gtttcaactt gtgcatacgc accaagatga ctttaaggaa 2160 aacaatagcg atcagggaag atacttcgaa agcagcaatc tcaccaacct ttctctgcct 2220 atcggcatca agtttgagag atttgctaac aacgatacag cttcttatca tgtcactgct 2280 gcttattctc ctgatatcgt aagaagtaac cctgactgta ctacttctct gttagtaagc 2340 cccgactctg ctgtctgggt aacgaaagcc aacaaccttg cgcgaagcgc cttcatgcta 2400 caagcaggaa actacttgtc tttaagtcac aacatagaaa tcttcagcca gttcggtttc 2460 gagctcaggg gatcttcacg aacctataac gtagatctcg gatcgaagat ccagttctaa 2520 23 839 PRT Chlamydia psittaci 23 Met Lys His Pro Val Tyr Trp Phe Leu Ile Ser Ser Ser Leu Phe Ala 1 5 10 15 Ser Asn Ser Leu Ser Phe Ala Asn Asp Ala Gln Thr Ala Leu Thr Pro 20 25 30 Ser Asp Ser Tyr Asn Gly Asn Val Thr Ser Glu Glu Phe Gln Val Lys 35 40 45 Glu Thr Ser Ser Gly Thr Thr Tyr Thr Cys Glu Gly Asn Val Cys Ile 50 55 60 Ser Phe Ala Gly Lys Asp Ser Gly Leu Lys Lys Ser Cys Phe Ser Ala 65 70 75 80 Thr Asp Asn Leu Thr Phe Leu Gly Asn Gly Tyr Thr Leu Cys Phe Asp 85 90 95 Asn Ile Thr Thr Thr Ala Ser Asn Pro Gly Ala Ile Asn Val Gln Gly 100 105 110 Gln Gly Lys Thr Leu Gly Ile Ser Gly Phe Ser Leu Phe Ser Cys Ala 115 120 125 Tyr Cys Pro Pro Gly Thr Thr Gly Tyr Gly Ala Ile Gln Thr Lys Gly 130 135 140 Asn Thr Thr Leu Lys Asp Asn Ser Ser Leu Val Phe His Lys Asn Cys 145 150 155 160 Ser Thr Ala Glu Gly Gly Ala Ile Gln Cys Lys Gly Ser Ser Asp Ala 165 170 175 Glu Leu Lys Ile Glu Asn Asn Gln Asn Leu Val Phe Ser Glu Asn Ser 180 185 190 Ser Thr Ser Lys Gly Gly Ala Ile Tyr Ala Asp Lys Leu Thr Ile Val 195 200 205 Ser Gly Gly Pro Thr Leu Phe Ser Asn Asn Ser Val Ser Asn Gly Ser 210 215 220 Ser Pro Lys Gly Gly Ala Ile Ser Ile Lys Asp Ser Ser Gly Glu Cys 225 230 235 240 Ser Leu Thr Ala Asp Leu Gly Asp Ile Thr Phe Asp Gly Asn Lys Ile 245 250 255 Ile Lys Thr Ser Gly Gly Ser Ser Thr Val Thr Arg Asn Ser Ile Asp 260 265 270 Leu Gly Thr Gly Lys Phe Thr Lys Leu Arg Ala Lys Asp Gly Phe Gly 275 280 285 Ile Phe Phe Tyr Asp Pro Ile Thr Gly Gly Gly Ser Asp Glu Leu Asn 290 295 300 Ile Asn Lys Lys Glu Thr Val Asp Tyr Thr Gly Lys Ile Val Phe Ser 305 310 315 320 Gly Glu Lys Leu Ser Asp Glu Glu Lys Ala Arg Ala Glu Asn Leu Ala 325 330 335 Ser Thr Phe Asn Gln Pro Ile Thr Leu Ser Ala Gly Ser Leu Val Leu 340 345 350 Lys Asp Gly Val Ser Val Thr Ala Lys Gln Val Thr Gln Glu Ala Gly 355 360 365 Ser Thr Val Val Met Asp Leu Gly Thr Thr Leu Gln Thr Pro Ser Ser 370 375 380 Gly Gly Glu Thr Ile Thr Leu Thr Asn Leu Asp Ile Asn Ile Ala Ser 385 390 395 400 Leu Gly Gly Gly Gly Gly Thr Ser Pro Ala Lys Leu Ala Thr Asn Thr 405 410 415 Ala Ser Gln Ala Ile Thr Ile Asn Ala Val Asn Leu Val Asp Ala Asp 420 425 430 Gly Asn Ala Tyr Glu Asp Pro Ile Leu Ala Thr Ser Lys Pro Phe Thr 435 440 445 Ala Ile Val Ala Thr Thr Asn Ala Ser Thr Val Thr Gln Pro Thr Asp 450 455 460 Asn Leu Thr Asn Tyr Val Pro Pro Thr His Tyr Gly Tyr Gln Gly Asn 465 470 475 480 Trp Thr Val Thr Trp Asp Thr Glu Thr Ala Thr Lys Thr Ala Thr Leu 485 490 495 Thr Trp Glu Gln Thr Gly Tyr Ser Pro Asn Pro Glu Arg Gln Gly Pro 500 505 510 Leu Val Pro Asn Thr Leu Trp Gly Ala Phe Ser Asp Leu Arg Ala Ile 515 520 525 Gln Asn Leu Met Asp Ile Ser Val Asn Gly Ala Asp Tyr His Arg Gly 530 535 540 Phe Trp Val Ser Gly Leu Ala Asn Phe Leu His Lys Ser Gly Ser Asp 545 550 555 560 Thr Lys Arg Lys Phe Arg His Asn Ser Ala Gly Tyr Ala Leu Gly Val 565 570 575 Tyr Ala Lys Thr Pro Ser Asp Asp Ile Phe Ser Ala Ala Phe Cys Gln 580 585 590 Leu Phe Gly Lys Asp Lys Asp Tyr Leu Val Ser Lys Asn Asn Ala Asn 595 600 605 Ile Tyr Ala Gly Ser Leu Tyr Tyr Gln His Ile Ser Tyr Trp Ser Ala 610 615 620 Trp Gln Asn Leu Leu Gln Asn Thr Ile Gly Ala Glu Ala Pro Leu Val 625 630 635 640 Leu Asn Ala Gln Leu Thr Tyr Cys His Ala Ser Asn Asp Met Lys Thr 645 650 655 Asn Met Thr Thr Thr Tyr Ala Pro Arg Lys Thr Thr Tyr Ala Glu Ile 660 665 670 Lys Gly Asp Trp Gly Asn Asp Cys Phe Gly Val Glu Leu Gly Ala Thr 675 680 685 Val Pro Ile Gln Thr Glu Ser Ser Leu Leu Phe Asp Met Tyr Ser Pro 690 695 700 Phe Leu Lys Phe Gln Leu Val His Thr His Gln Asp Asp Phe Lys Glu 705 710 715 720 Asn Asn Ser Asp Gln Gly Arg Tyr Phe Glu Ser Ser Asn Leu Thr Asn 725 730 735 Leu Ser Leu Pro Ile Gly Ile Lys Phe Glu Arg Phe Ala Asn Asn Asp 740 745 750 Thr Ala Ser Tyr His Val Thr Ala Ala Tyr Ser Pro Asp Ile Val Arg 755 760 765 Ser Asn Pro Asp Cys Thr Thr Ser Leu Leu Val Ser Pro Asp Ser Ala 770 775 780 Val Trp Val Thr Lys Ala Asn Asn Leu Ala Arg Ser Ala Phe Met Leu 785 790 795 800 Gln Ala Gly Asn Tyr Leu Ser Leu Ser His Asn Ile Glu Ile Phe Ser 805 810 815 Gln Phe Gly Phe Glu Leu Arg Gly Ser Ser Arg Thr Tyr Asn Val Asp 820 825 830 Leu Gly Ser Lys Ile Gln Phe 835 24 1039 DNA Chlamydia psittaci 24 aaacgttttc atattaatgg ggttcctgaa tggtctttat ctacgcctta ttctcttgct 60 atggggtata atatcttggc tacgggagtg cagatggtta aagcctatgc cattcttgcc 120 aacggtggtt atgatgtgcg ccctaccttg ataaaaaaaa tagtcactac ttctggaaaa 180 gagtacgtgt tgcatcctca agttcgtgga gaaagaattc tttctcagga cattgtggat 240 gaggtattga aagctacgcg ttttactacc tatcctggag gaacgggatt tcgggctgcg 300 cctaaaaagc attccagtgc agggaaaaca ggaacaacag aaaagctagt tcatggaaag 360 tatgataagc atcggcatat ttcttcattt ataggtatca cgccgatata cccttcggca 420 ggggggagtg ttcctttggt catgcttgtc tctatcagtt atacgaccga caacggtagt 480 caagtgtacg tcgttcaatt gcgacatgag ggtatcgaaa tctgtcgtca attcgtccat 540 gttaacctaa ttgtgtggtc attatcgctt tctttatact acttaccgta gttcctacgg 600 atactagcaa aaagttctgc tctttgcgtt gctctttgaa cagcatactg tacttttaaa 660 aagtctgcta aattttcccg ttctccattc ctatctgaga agtagagaag ggctctattt 720 aacacttctt ctccagaaga cacccaattg accatcttac gggcaacgga ctcgtgttct 780 tcttcttttt tggtttgtaa gttttgttgc gtatgctcag ctatatcatt cagatcacca 840 ttgattaaat caatgatcac actgacagct tcaaaatgtt cttgcgatag tttattttga 900 tcttgttgta gagtggattg tgcatcccat aaacgctctt ttagattgtt tatttgctct 960 ttcagctctt ccgaatctaa cgcctcttcc agttcaggat cgataatgtt agagtttctg 1020 tcttgcatca tcgccatag 1039 25 196 PRT Chlamydia psittaci 25 Lys Arg Phe His Ile Asn Gly Val Pro Glu Trp Ser Leu Ser Thr Pro 1 5 10 15 Tyr Ser Leu Ala Met Gly Tyr Asn Ile Leu Ala Thr Gly Val Gln Met 20 25 30 Val Lys Ala Tyr Ala Ile Leu Ala Asn Gly Gly Tyr Asp Val Arg Pro 35 40 45 Thr Leu Ile Lys Lys Ile Val Thr Thr Ser Gly Lys Glu Tyr Val Leu 50 55 60 His Pro Gln Val Arg Gly Glu Arg Ile Leu Ser Gln Asp Ile Val Asp 65 70 75 80 Glu Val Leu Lys Ala Thr Arg Phe Thr Thr Tyr Pro Gly Gly Thr Gly 85 90 95 Phe Arg Ala Ala Pro Lys Lys His Ser Ser Ala Gly Lys Thr Gly Thr 100 105 110 Thr Glu Lys Leu Val His Gly Lys Tyr Asp Lys His Arg His Ile Ser 115 120 125 Ser Phe Ile Gly Ile Thr Pro Ile Tyr Pro Ser Ala Gly Gly Ser Val 130 135 140 Pro Leu Val Met Leu Val Ser Ile Ser Tyr Thr Thr Asp Asn Gly Ser 145 150 155 160 Gln Val Tyr Val Val Gln Leu Arg His Glu Gly Ile Glu Ile Cys Arg 165 170 175 Gln Phe Val His Val Asn Leu Ile Val Trp Ser Leu Ser Leu Ser Leu 180 185 190 Tyr Tyr Leu Pro 195 26 1950 DNA Chlamydia psittaci 26 atgaatcacc gtaaatgctt aaccatgatt acctatggag ttctgctctc ctattctttc 60 ctgatcatac ggtattataa aattcagatt tgtgaggaga aacgttgggc agcagaagct 120 ttaggacaac atgaatttcg agtaaaggac ccttttcgta gggggacgtt tttttctcag 180 atgaatttac gtaagggaga ttcagagcaa cgacaagctc tggccgtgga cattacgaaa 240 tttcatcttt gtttagatgc tgtagctgtt cctgaagaac accgtgatgt gattgctaag 300 aaagttttta gtctcattgg agaaggtgat tatgacaaac tccgtgcgga gtttgataaa 360 aaatctcgct atcgaaagtt atttctttgg ttagatcgtg cggatcatga ccgcatcctg 420 tcttggtggc gggggtacgc agcaaaatct aaaataccct cgaatgcttt gtttttcatg 480 accgactatc aaagatctta tccctttggc aaacttttag gccaagttct acatactctg 540 agagaagtca aggatgagaa aacaggcaaa gctttcccta caggaggttt agaagcctat 600 tttaaccacg tccttgaagg agagccagga gaacggaaat tcctacgttc tcctttaaat 660 cgtttagatc tagataaagt cacaaagatt cctagggatg gttcggatat ttatctcaca 720 gtcaatccct gtatacagac tatagcggaa gaggaattag aaaaaggggt aaaggaagcc 780 aaagctaaag gtgggcgtct aattttaatg aatgcttata caggcgagat tcttgcttta 840 gcacagtatc ctttctttaa tccttcggaa tacaaggaat ttttcaatga taaggaaaaa 900 atagagcaca caaaagtaac atcagtcagt gatgtgtttg aacccggctc tatcatgaaa 960 cctctgactc tggctatagc gttgctggcc aacgaagaga tggtgaaaag atcaggaaag 1020 cccttatttg atcctaatga acctatagat gtaacccgca ggattttccc aggaagaaag 1080 caatttccgc ttaaggatat ctcatcgaat cggcgtttaa atatgtacat ggcgattcaa 1140 aagtcttcga acgtttatgt agcgcaactt gctgatctta tagtgcaaca tctagggaac 1200 cactggtatg aagacaagtt attgttatta ggatttggta aaaagacggg gatagaattg 1260 ccaggggaag cgtcaggatt ggtaccttca cctaaacgtt ttcatattaa tggggttcct 1320 gaatggtctt tatctacgcc ttattctctt gctatggggt ataatatctt ggctacggga 1380 gtgcagatgg ttaaagccta tgccattctt gccaacggtg gttatgatgt gcgccctacc 1440 ttgataaaaa aaatagtcac tacttctgga aaagagtacg tgttgcatcc tcaagttcgt 1500 ggagaaagaa ttctttctca ggacattgtg gatgaggtat tgaaagctac gcgttttact 1560 acctatcctg gaggaacggg atttcgggct gcgcctaaaa agcattccag tgcagggaaa 1620 acaggaacaa cagaaaagct agttcatgga aagtatgata agcatcggca tatttcttca 1680 tttataggta tcacgccgat atacccttcg gcagggggga gtgttccttt ggtcatgctt 1740 gtctctatag atgatcctga tcattgtgtt cgcgaggatg gaacaaagaa ctatatggga 1800 ggccgatgtg ccgcccctgt atttggcaga gttgcggatc gtgttttatc ttatctagga 1860 gttcccgaag ataaagaaaa atacagttat cagagtgagg tggctgctat gaaagctttg 1920 tatgaggaat ggaatcgttc ggggaaataa 1950 27 649 PRT Chlamydia psittaci 27 Met Asn His Arg Lys Cys Leu Thr Met Ile Thr Tyr Gly Val Leu Leu 1 5 10 15 Ser Tyr Ser Phe Leu Ile Ile Arg Tyr Tyr Lys Ile Gln Ile Cys Glu 20 25 30 Glu Lys Arg Trp Ala Ala Glu Ala Leu Gly Gln His Glu Phe Arg Val 35 40 45 Lys Asp Pro Phe Arg Arg Gly Thr Phe Phe Ser Gln Met Asn Leu Arg 50 55 60 Lys Gly Asp Ser Glu Gln Arg Gln Ala Leu Ala Val Asp Ile Thr Lys 65 70 75 80 Phe His Leu Cys Leu Asp Ala Val Ala Val Pro Glu Glu His Arg Asp 85 90 95 Val Ile Ala Lys Lys Val Phe Ser Leu Ile Gly Glu Gly Asp Tyr Asp 100 105 110 Lys Leu Arg Ala Glu Phe Asp Lys Lys Ser Arg Tyr Arg Lys Leu Phe 115 120 125 Leu Trp Leu Asp Arg Ala Asp His Asp Arg Ile Leu Ser Trp Trp Arg 130 135 140 Gly Tyr Ala Ala Lys Ser Lys Ile Pro Ser Asn Ala Leu Phe Phe Met 145 150 155 160 Thr Asp Tyr Gln Arg Ser Tyr Pro Phe Gly Lys Leu Leu Gly Gln Val 165 170 175 Leu His Thr Leu Arg Glu Val Lys Asp Glu Lys Thr Gly Lys Ala Phe 180 185 190 Pro Thr Gly Gly Leu Glu Ala Tyr Phe Asn His Val Leu Glu Gly Glu 195 200 205 Pro Gly Glu Arg Lys Phe Leu Arg Ser Pro Leu Asn Arg Leu Asp Leu 210 215 220 Asp Lys Val Thr Lys Ile Pro Arg Asp Gly Ser Asp Ile Tyr Leu Thr 225 230 235 240 Val Asn Pro Cys Ile Gln Thr Ile Ala Glu Glu Glu Leu Glu Lys Gly 245 250 255 Val Lys Glu Ala Lys Ala Lys Gly Gly Arg Leu Ile Leu Met Asn Ala 260 265 270 Tyr Thr Gly Glu Ile Leu Ala Leu Ala Gln Tyr Pro Phe Phe Asn Pro 275 280 285 Ser Glu Tyr Lys Glu Phe Phe Asn Asp Lys Glu Lys Ile Glu His Thr 290 295 300 Lys Val Thr Ser Val Ser Asp Val Phe Glu Pro Gly Ser Ile Met Lys 305 310 315 320 Pro Leu Thr Leu Ala Ile Ala Leu Leu Ala Asn Glu Glu Met Val Lys 325 330 335 Arg Ser Gly Lys Pro Leu Phe Asp Pro Asn Glu Pro Ile Asp Val Thr 340 345 350 Arg Arg Ile Phe Pro Gly Arg Lys Gln Phe Pro Leu Lys Asp Ile Ser 355 360 365 Ser Asn Arg Arg Leu Asn Met Tyr Met Ala Ile Gln Lys Ser Ser Asn 370 375 380 Val Tyr Val Ala Gln Leu Ala Asp Leu Ile Val Gln His Leu Gly Asn 385 390 395 400 His Trp Tyr Glu Asp Lys Leu Leu Leu Leu Gly Phe Gly Lys Lys Thr 405 410 415 Gly Ile Glu Leu Pro Gly Glu Ala Ser Gly Leu Val Pro Ser Pro Lys 420 425 430 Arg Phe His Ile Asn Gly Val Pro Glu Trp Ser Leu Ser Thr Pro Tyr 435 440 445 Ser Leu Ala Met Gly Tyr Asn Ile Leu Ala Thr Gly Val Gln Met Val 450 455 460 Lys Ala Tyr Ala Ile Leu Ala Asn Gly Gly Tyr Asp Val Arg Pro Thr 465 470 475 480 Leu Ile Lys Lys Ile Val Thr Thr Ser Gly Lys Glu Tyr Val Leu His 485 490 495 Pro Gln Val Arg Gly Glu Arg Ile Leu Ser Gln Asp Ile Val Asp Glu 500 505 510 Val Leu Lys Ala Thr Arg Phe Thr Thr Tyr Pro Gly Gly Thr Gly Phe 515 520 525 Arg Ala Ala Pro Lys Lys His Ser Ser Ala Gly Lys Thr Gly Thr Thr 530 535 540 Glu Lys Leu Val His Gly Lys Tyr Asp Lys His Arg His Ile Ser Ser 545 550 555 560 Phe Ile Gly Ile Thr Pro Ile Tyr Pro Ser Ala Gly Gly Ser Val Pro 565 570 575 Leu Val Met Leu Val Ser Ile Asp Asp Pro Asp His Cys Val Arg Glu 580 585 590 Asp Gly Thr Lys Asn Tyr Met Gly Gly Arg Cys Ala Ala Pro Val Phe 595 600 605 Gly Arg Val Ala Asp Arg Val Leu Ser Tyr Leu Gly Val Pro Glu Asp 610 615 620 Lys Glu Lys Tyr Ser Tyr Gln Ser Glu Val Ala Ala Met Lys Ala Leu 625 630 635 640 Tyr Glu Glu Trp Asn Arg Ser Gly Lys 645 28 960 DNA Chlamydia psittaci 28 atgttcaata agctcattga aacagcacag aaacgggtgg aagcaagaaa ctatactatt 60 cgaaagcata ctcttgagta tgacgatgtt atgaataggc aaaggcagac gatctatgct 120 tttcgtaatg acgttatccg ctctgaagat atctttggtt tagctaagga agcaatatct 180 catgttgcat taatgatcgc ttcgttgata gtgagccgtg atcatcctac agggaattct 240 cttcctaggc tggaagaatg gatgaactat tctttcccac tgcaattgaa tattgaagaa 300 ttgaaaagat tgaagtctat agatgccatt gccgaacggg ttgctgatga tctcatagaa 360 gttttccaga ataagtttgc ttctatggtg caggaaatta ccgaagcagc cggagaaaaa 420 gtcgatgcta atggtgtctg taaagatgtt attcgctcgg tcatgattat gcatatcgat 480 gagcagtgga aaattcatct tgtagatatg gatttattac gtagtgaagt aggtttacgt 540 actgtcggtc agaaagaccc tcttatcgaa tttaaacatg agtcgttctt actattcgaa 600 agtcttattc gcgatattcg tattgctatt gtaaagcatt tgttccgttt agagttgacg 660 atgactagag aacagcggcc tcaaaatgtc gtgcctgttg ttgccacatc tttccaaaat 720 aatgaaaatt tcggtccttt ggaactcaca gttatcagtg attctgacga tgaataaaaa 780 gagctttagg gctgggctag cttccagcct tttcccttac gttattgatt tatagtttta 840 aataaatacg gaccactcag accaggattg tgtgtcgtgg tggcgtatcc aaaatgttct 900 gtgattatcc tcaatcagaa attgtacatg atgatcgcga ttgcgtgttg tcatgcaaat 960 29 258 PRT Chlamydia psittaci 29 Met Phe Asn Lys Leu Ile Glu Thr Ala Gln Lys Arg Val Glu Ala Arg 1 5 10 15 Asn Tyr Thr Ile Arg Lys His Thr Leu Glu Tyr Asp Asp Val Met Asn 20 25 30 Arg Gln Arg Gln Thr Ile Tyr Ala Phe Arg Asn Asp Val Ile Arg Ser 35 40 45 Glu Asp Ile Phe Gly Leu Ala Lys Glu Ala Ile Ser His Val Ala Leu 50 55 60 Met Ile Ala Ser Leu Ile Val Ser Arg Asp His Pro Thr Gly Asn Ser 65 70 75 80 Leu Pro Arg Leu Glu Glu Trp Met Asn Tyr Ser Phe Pro Leu Gln Leu 85 90 95 Asn Ile Glu Glu Leu Lys Arg Leu Lys Ser Ile Asp Ala Ile Ala Glu 100 105 110 Arg Val Ala Asp Asp Leu Ile Glu Val Phe Gln Asn Lys Phe Ala Ser 115 120 125 Met Val Gln Glu Ile Thr Glu Ala Ala Gly Glu Lys Val Asp Ala Asn 130 135 140 Gly Val Cys Lys Asp Val Ile Arg Ser Val Met Ile Met His Ile Asp 145 150 155 160 Glu Gln Trp Lys Ile His Leu Val Asp Met Asp Leu Leu Arg Ser Glu 165 170 175 Val Gly Leu Arg Thr Val Gly Gln Lys Asp Pro Leu Ile Glu Phe Lys 180 185 190 His Glu Ser Phe Leu Leu Phe Glu Ser Leu Ile Arg Asp Ile Arg Ile 195 200 205 Ala Ile Val Lys His Leu Phe Arg Leu Glu Leu Thr Met Thr Arg Glu 210 215 220 Gln Arg Pro Gln Asn Val Val Pro Val Val Ala Thr Ser Phe Gln Asn 225 230 235 240 Asn Glu Asn Phe Gly Pro Leu Glu Leu Thr Val Ile Ser Asp Ser Asp 245 250 255 Asp Glu 30 697 DNA Chlamydia psittaci 30 gggtttgatt atctcagaga taattctatt gcaacttctg tggatgagca ggtgggacgt 60 gggttttatt ttgctattat cgatgaagtc gactcgattt taattgatga agccagaact 120 cctttaatta tttctggtcc tggggaaaaa cataatcctg tgtatttcga actcaaagat 180 aaagtggctg acctcgttca gttacaaagg gagttatgta accagttagc tcttgaagct 240 agacggggac tagaattgtt cttggatatg gatattcttc ctaaggataa aaaagttatc 300 gaagctatct ccgaattttg ccgtagctta tggttagtta gtaagggaat gcctttaaat 360 cgtgttttgc gtagagtgcg cgaacaccca gatttgcgag ccatgataga taaatgggat 420 acttattatc atgctgagca aaataaagaa gagagtatag agaagctatc tcagctgtat 480 atcattgttg atgaacataa taacgatttt gaattgacag atcgtggcat gcaacaatgg 540 gtggataagg ctggaggttc tgctgaagat tttgtcatga tggacatggg gcatgaatat 600 gctcttatag atggtgacga taccttatca ccgacagaga aaatcaatag aaaaatagct 660 atttccgaag aagatacgag gagaaaagct cgagctc 697 31 232 PRT Chlamydia psittaci 31 Gly Phe Asp Tyr Leu Arg Asp Asn Ser Ile Ala Thr Ser Val Asp Glu 1 5 10 15 Gln Val Gly Arg Gly Phe Tyr Phe Ala Ile Ile Asp Glu Val Asp Ser 20 25 30 Ile Leu Ile Asp Glu Ala Arg Thr Pro Leu Ile Ile Ser Gly Pro Gly 35 40 45 Glu Lys His Asn Pro Val Tyr Phe Glu Leu Lys Asp Lys Val Ala Asp 50 55 60 Leu Val Gln Leu Gln Arg Glu Leu Cys Asn Gln Leu Ala Leu Glu Ala 65 70 75 80 Arg Arg Gly Leu Glu Leu Phe Leu Asp Met Asp Ile Leu Pro Lys Asp 85 90 95 Lys Lys Val Ile Glu Ala Ile Ser Glu Phe Cys Arg Ser Leu Trp Leu 100 105 110 Val Ser Lys Gly Met Pro Leu Asn Arg Val Leu Arg Arg Val Arg Glu 115 120 125 His Pro Asp Leu Arg Ala Met Ile Asp Lys Trp Asp Thr Tyr Tyr His 130 135 140 Ala Glu Gln Asn Lys Glu Glu Ser Ile Glu Lys Leu Ser Gln Leu Tyr 145 150 155 160 Ile Ile Val Asp Glu His Asn Asn Asp Phe Glu Leu Thr Asp Arg Gly 165 170 175 Met Gln Gln Trp Val Asp Lys Ala Gly Gly Ser Ala Glu Asp Phe Val 180 185 190 Met Met Asp Met Gly His Glu Tyr Ala Leu Ile Asp Gly Asp Asp Thr 195 200 205 Leu Ser Pro Thr Glu Lys Ile Asn Arg Lys Ile Ala Ile Ser Glu Glu 210 215 220 Asp Thr Arg Arg Lys Ala Arg Ala 225 230 32 2910 DNA Chlamydia psittaci 32 atgttagatt ttcttaaacg tttctttgga tcttctcaag agcgcacctt aaaaaaattt 60 caaaaacttg tggataaggt caacctctat gatgagatgc tagctccttt gtctgatgag 120 gagttacgta ataaaacagc agagttaaaa aagcgttatc aggacggcga atccttagat 180 gatatgcttc ccgaggctta tgccgtagtg aaaaatgtat gcaggcgttt aacaggaact 240 cctgtagaag tgtcgggtta tcatcaaaat tgggacatgg ttccctatga tgtgcaggtt 300 ctcggtgcta tagctatgca taagggcttt ataaccgaga tgcagacagg agaggggaaa 360 actctcaccg ctgttatgcc tctatattta aatgcattga caggcaagcc tgtgcattta 420 gtcacagtga atgattatct cgctcaaagg gattgtgagt gggtcggctc tatattgcgt 480 tggttaggtt taactaccgg agtattgata tcaggatcgc ctttagaaaa aagaaaagac 540 atttatcgtt gtgacgttgt ctacggtaca gcatcagagt tcgggtttga ttatctcaga 600 gataattcta ttgcaacttc tgtggatgag caggtgggac gtgggtttta ttttgctatt 660 atcgatgaag tcgactcgat tttaattgat gaagccagaa ctcctttaat tatttctggt 720 cctggggaaa aacataatcc tgtgtatttc gaactcaaag ataaagtggc tgacctcgtt 780 cagttacaaa gggagttatg taaccagtta gctcttgaag ctagacgggg actagaattg 840 ttcttggata tggatattct tcctaaggat aaaaaagtta tcgaagctat ctccgaattt 900 tgccgtagct tatggttagt tagtaaggga atgcctttaa atcgtgtttt gcgtagagtg 960 cgcgaacacc cagatttgcg agccatgata gataaatggg atacttatta tcatgctgag 1020 caaaataaag aagagagtat agagaagcta tctcagctgt atatcattgt tgatgaacat 1080 aataacgatt ttgaattgac agatcgtggc atgcaacaat gggtggataa ggctggaggt 1140 tctgctgaag attttgtcat gatggacatg gggcatgaat atgctcttat agatggtgac 1200 gataccttat caccgacaga gaaaatcaat agaaaaatag ctatttccga agaagatacg 1260 aggagaaaag ctcgagctca tggcttgcgc caactattaa gagcgcatct tcttatggaa 1320 cgcgatgtgg attatattgt tcgtaatgat caaattgtca tcattgacga acatacgggc 1380 cgcccgcaac caggtcgtcg tttttccgaa ggactgcatc aagccataga agcaaaagaa 1440 catgtcacta tccgtaagga atcacaaacg tttgctacag ttaccttaca gaatttcttc 1500 cgtctgtatg aaaaactcgc aggtatgacg ggaacagcaa ttacggaatc taaagagttt 1560 aaagagattt ataatcttta tgtattgcag gtgcccacgt ttaaagaatg tttgcgtgta 1620 gatcacaatg acgaatttta tatgacagag cgtgaaaagt accacgcgat tgttaaggaa 1680 attgcccgta tacatgccgt agggaacccg attctcatag gaacggagtc tgtagaggtt 1740 tctgagaaac tttctcgtat tttgagacaa aatcgcatag aacatacagt gttaaatgcg 1800 aaaaatcatg ctcaagaagc agagatcatt gcagcagcag gaaagctggg agctgtgact 1860 gtagctacca atatggctgg ccgtggtaca gatattaagc tggatgaaga agctgtagtt 1920 gttggaggtc tccatgttat tggtacgagt cggcaccaat cacgccgtat agataggcag 1980 ttgcgcgggc gttgcgcacg tttaggagat cctggttcgg cgaaattttt cctatctttt 2040 gaagatcgcc tgatgcgctt atttgcatcg cccaagttaa atgccttgat tcgtcatttc 2100 cgtcctcctg aaggagaggc tatgtcggat cctatgttca ataagctcat tgaaacagca 2160 cagaaacggg tggaagcaag aaactatact attcgaaagc atactcttga gtatgacgat 2220 gttatgaata ggcaaaggca gacgatctat gcttttcgta atgacgttat ccgctctgaa 2280 gatatctttg gtttagctaa ggaagcaata tctcatgttg cattaatgat cgcttcgttg 2340 atagtgagcc gtgatcatcc tacagggaat tctcttccta ggctggaaga atggatgaac 2400 tattctttcc cactgcaatt gaatattgaa gaattgaaaa gattgaagtc tatagatgcc 2460 attgccgaac gggttgctga tgatctcata gaagttttcc agaataagtt tgcttctatg 2520 gtgcaggaaa ttaccgaagc agccggagaa aaagtcgatg ctaatggtgt ctgtaaagat 2580 gttattcgct cggtcatgat tatgcatatc gatgagcagt ggaaaattca tcttgtagat 2640 atggatttat tacgtagtga agtaggttta cgtactgtcg gtcagaaaga ccctcttatc 2700 gaatttaaac atgagtcgtt cttactattc gaaagtctta ttcgcgatat tcgtattgct 2760 attgtaaagc atttgttccg tttagagttg acgatgacta gagaacagcg gcctcaaaat 2820 gtcgtgcctg ttgttgccac atctttccaa aataatgaaa atttcggtcc tttggaactc 2880 acagttatca gtgattctga cgatgaataa 2910 33 969 PRT Chlamydia psittaci 33 Met Leu Asp Phe Leu Lys Arg Phe Phe Gly Ser Ser Gln Glu Arg Thr 1 5 10 15 Leu Lys Lys Phe Gln Lys Leu Val Asp Lys Val Asn Leu Tyr Asp Glu 20 25 30 Met Leu Ala Pro Leu Ser Asp Glu Glu Leu Arg Asn Lys Thr Ala Glu 35 40 45 Leu Lys Lys Arg Tyr Gln Asp Gly Glu Ser Leu Asp Asp Met Leu Pro 50 55 60 Glu Ala Tyr Ala Val Val Lys Asn Val Cys Arg Arg Leu Thr Gly Thr 65 70 75 80 Pro Val Glu Val Ser Gly Tyr His Gln Asn Trp Asp Met Val Pro Tyr 85 90 95 Asp Val Gln Val Leu Gly Ala Ile Ala Met His Lys Gly Phe Ile Thr 100 105 110 Glu Met Gln Thr Gly Glu Gly Lys Thr Leu Thr Ala Val Met Pro Leu 115 120 125 Tyr Leu Asn Ala Leu Thr Gly Lys Pro Val His Leu Val Thr Val Asn 130 135 140 Asp Tyr Leu Ala Gln Arg Asp Cys Glu Trp Val Gly Ser Ile Leu Arg 145 150 155 160 Trp Leu Gly Leu Thr Thr Gly Val Leu Ile Ser Gly Ser Pro Leu Glu 165 170 175 Lys Arg Lys Asp Ile Tyr Arg Cys Asp Val Val Tyr Gly Thr Ala Ser 180 185 190 Glu Phe Gly Phe Asp Tyr Leu Arg Asp Asn Ser Ile Ala Thr Ser Val 195 200 205 Asp Glu Gln Val Gly Arg Gly Phe Tyr Phe Ala Ile Ile Asp Glu Val 210 215 220 Asp Ser Ile Leu Ile Asp Glu Ala Arg Thr Pro Leu Ile Ile Ser Gly 225 230 235 240 Pro Gly Glu Lys His Asn Pro Val Tyr Phe Glu Leu Lys Asp Lys Val 245 250 255 Ala Asp Leu Val Gln Leu Gln Arg Glu Leu Cys Asn Gln Leu Ala Leu 260 265 270 Glu Ala Arg Arg Gly Leu Glu Leu Phe Leu Asp Met Asp Ile Leu Pro 275 280 285 Lys Asp Lys Lys Val Ile Glu Ala Ile Ser Glu Phe Cys Arg Ser Leu 290 295 300 Trp Leu Val Ser Lys Gly Met Pro Leu Asn Arg Val Leu Arg Arg Val 305 310 315 320 Arg Glu His Pro Asp Leu Arg Ala Met Ile Asp Lys Trp Asp Thr Tyr 325 330 335 Tyr His Ala Glu Gln Asn Lys Glu Glu Ser Ile Glu Lys Leu Ser Gln 340 345 350 Leu Tyr Ile Ile Val Asp Glu His Asn Asn Asp Phe Glu Leu Thr Asp 355 360 365 Arg Gly Met Gln Gln Trp Val Asp Lys Ala Gly Gly Ser Ala Glu Asp 370 375 380 Phe Val Met Met Asp Met Gly His Glu Tyr Ala Leu Ile Asp Gly Asp 385 390 395 400 Asp Thr Leu Ser Pro Thr Glu Lys Ile Asn Arg Lys Ile Ala Ile Ser 405 410 415 Glu Glu Asp Thr Arg Arg Lys Ala Arg Ala His Gly Leu Arg Gln Leu 420 425 430 Leu Arg Ala His Leu Leu Met Glu Arg Asp Val Asp Tyr Ile Val Arg 435 440 445 Asn Asp Gln Ile Val Ile Ile Asp Glu His Thr Gly Arg Pro Gln Pro 450 455 460 Gly Arg Arg Phe Ser Glu Gly Leu His Gln Ala Ile Glu Ala Lys Glu 465 470 475 480 His Val Thr Ile Arg Lys Glu Ser Gln Thr Phe Ala Thr Val Thr Leu 485 490 495 Gln Asn Phe Phe Arg Leu Tyr Glu Lys Leu Ala Gly Met Thr Gly Thr 500 505 510 Ala Ile Thr Glu Ser Lys Glu Phe Lys Glu Ile Tyr Asn Leu Tyr Val 515 520 525 Leu Gln Val Pro Thr Phe Lys Glu Cys Leu Arg Val Asp His Asn Asp 530 535 540 Glu Phe Tyr Met Thr Glu Arg Glu Lys Tyr His Ala Ile Val Lys Glu 545 550 555 560 Ile Ala Arg Ile His Ala Val Gly Asn Pro Ile Leu Ile Gly Thr Glu 565 570 575 Ser Val Glu Val Ser Glu Lys Leu Ser Arg Ile Leu Arg Gln Asn Arg 580 585 590 Ile Glu His Thr Val Leu Asn Ala Lys Asn His Ala Gln Glu Ala Glu 595 600 605 Ile Ile Ala Ala Ala Gly Lys Leu Gly Ala Val Thr Val Ala Thr Asn 610 615 620 Met Ala Gly Arg Gly Thr Asp Ile Lys Leu Asp Glu Glu Ala Val Val 625 630 635 640 Val Gly Gly Leu His Val Ile Gly Thr Ser Arg His Gln Ser Arg Arg 645 650 655 Ile Asp Arg Gln Leu Arg Gly Arg Cys Ala Arg Leu Gly Asp Pro Gly 660 665 670 Ser Ala Lys Phe Phe Leu Ser Phe Glu Asp Arg Leu Met Arg Leu Phe 675 680 685 Ala Ser Pro Lys Leu Asn Ala Leu Ile Arg His Phe Arg Pro Pro Glu 690 695 700 Gly Glu Ala Met Ser Asp Pro Met Phe Asn Lys Leu Ile Glu Thr Ala 705 710 715 720 Gln Lys Arg Val Glu Ala Arg Asn Tyr Thr Ile Arg Lys His Thr Leu 725 730 735 Glu Tyr Asp Asp Val Met Asn Arg Gln Arg Gln Thr Ile Tyr Ala Phe 740 745 750 Arg Asn Asp Val Ile Arg Ser Glu Asp Ile Phe Gly Leu Ala Lys Glu 755 760 765 Ala Ile Ser His Val Ala Leu Met Ile Ala Ser Leu Ile Val Ser Arg 770 775 780 Asp His Pro Thr Gly Asn Ser Leu Pro Arg Leu Glu Glu Trp Met Asn 785 790 795 800 Tyr Ser Phe Pro Leu Gln Leu Asn Ile Glu Glu Leu Lys Arg Leu Lys 805 810 815 Ser Ile Asp Ala Ile Ala Glu Arg Val Ala Asp Asp Leu Ile Glu Val 820 825 830 Phe Gln Asn Lys Phe Ala Ser Met Val Gln Glu Ile Thr Glu Ala Ala 835 840 845 Gly Glu Lys Val Asp Ala Asn Gly Val Cys Lys Asp Val Ile Arg Ser 850 855 860 Val Met Ile Met His Ile Asp Glu Gln Trp Lys Ile His Leu Val Asp 865 870 875 880 Met Asp Leu Leu Arg Ser Glu Val Gly Leu Arg Thr Val Gly Gln Lys 885 890 895 Asp Pro Leu Ile Glu Phe Lys His Glu Ser Phe Leu Leu Phe Glu Ser 900 905 910 Leu Ile Arg Asp Ile Arg Ile Ala Ile Val Lys His Leu Phe Arg Leu 915 920 925 Glu Leu Thr Met Thr Arg Glu Gln Arg Pro Gln Asn Val Val Pro Val 930 935 940 Val Ala Thr Ser Phe Gln Asn Asn Glu Asn Phe Gly Pro Leu Glu Leu 945 950 955 960 Thr Val Ile Ser Asp Ser Asp Asp Glu 965 34 577 DNA Chlamydia psittaci 34 gttgatgctg cagttattcc agggaacttc gccattgcag ggggaatctg tccgtataaa 60 aacagtctat acctagaaga tgtccgtact tcccaataca ccaatgtcgt tgtcatacgt 120 gctgaagata tggaagactc gagaatgcat aaactaaaac agctattgca aagcagttct 180 gtgcaggatt tctttaatac gaaatataag gggatctttt tatcgcagta acacatctgg 240 atggcttagg gaagagttga gccaccccgt tctccgtagg tttaaggcat attgggaaac 300 gattttcttg aattttttga aaaactttga ctgtttttct tttgattatt cgaagcagat 360 gtatgtcgag tatggcggtt ttagggccca gaggtccttt cagttctcct tttacatgtt 420 ctctataccc aacccaccta aaaatgcact tgctaggttc cattcctata gttggcatat 480 acattggagc gaagcggata gccgccgttg ctcaatatca tagaatgtgt agagcgaata 540 caggagtgtc tcaggtgatt attcaggatt caggatt 577 35 76 PRT Chlamydia psittaci 35 Val Asp Ala Ala Val Ile Pro Gly Asn Phe Ala Ile Ala Gly Gly Ile 1 5 10 15 Cys Pro Tyr Lys Asn Ser Leu Tyr Leu Glu Asp Val Arg Thr Ser Gln 20 25 30 Tyr Thr Asn Val Val Val Ile Arg Ala Glu Asp Met Glu Asp Ser Arg 35 40 45 Met His Lys Leu Lys Gln Leu Leu Gln Ser Ser Ser Val Gln Asp Phe 50 55 60 Phe Asn Thr Lys Tyr Lys Gly Ile Phe Leu Ser Gln 65 70 75 36 804 DNA Chlamydia psittaci 36 atgaaaaaaa tcacaatact ctcgttactt gctttagcca tctctttaac aggttgttgc 60 aagaattcag aaggagtctt gcggattgcg gcgagtccca cgccacatgc agagcttctt 120 tatagtttag aaaaggaggc tcaatccctt ggattgcaat tgaaaatact tcccatagat 180 gattaccgtg tacctaaccg tttgctttta gataagcaaa tagaggcaaa ttatttccaa 240 catgaagatt tcttaaaaga tgagtgtgct cggtaccaat gcgaaggaaa acttgcgatt 300 ttggctaagg tacatttaga acctatgggt ttatattcta ataaaaccca gtctctcgaa 360 gagcttaaag tcaaggaaca gctacgtata gcggttccta tagatagaac aaacgaacaa 420 cgtgcgctag acttattgcg agactgcaat ttgattagtt acaaagaagc ttctcatcta 480 gatatcaccg caaaagatgt ctttggttgt ggagggaaaa aggtaacgat tatagagatg 540 gcagcacctt tattagtatc ttctttacca gacgttgatg ctgcagttat tccagggaac 600 ttcgccattg cagggggaat ctgtccgtat aaaaacagtc tatacctaga agatgtccgt 660 acttcccaat acaccaatgt cgttgtcata cgtgctgaag atatggaaga ctcgagaatg 720 cataaactaa aacagctatt gcaaagcagt tctgtgcagg atttctttaa tacgaaatat 780 aaggggatct ttttatcgca gtaa 804 37 267 PRT Chlamydia psittaci 37 Met Lys Lys Ile Thr Ile Leu Ser Leu Leu Ala Leu Ala Ile Ser Leu 1 5 10 15 Thr Gly Cys Cys Lys Asn Ser Glu Gly Val Leu Arg Ile Ala Ala Ser 20 25 30 Pro Thr Pro His Ala Glu Leu Leu Tyr Ser Leu Glu Lys Glu Ala Gln 35 40 45 Ser Leu Gly Leu Gln Leu Lys Ile Leu Pro Ile Asp Asp Tyr Arg Val 50 55 60 Pro Asn Arg Leu Leu Leu Asp Lys Gln Ile Glu Ala Asn Tyr Phe Gln 65 70 75 80 His Glu Asp Phe Leu Lys Asp Glu Cys Ala Arg Tyr Gln Cys Glu Gly 85 90 95 Lys Leu Ala Ile Leu Ala Lys Val His Leu Glu Pro Met Gly Leu Tyr 100 105 110 Ser Asn Lys Thr Gln Ser Leu Glu Glu Leu Lys Val Lys Glu Gln Leu 115 120 125 Arg Ile Ala Val Pro Ile Asp Arg Thr Asn Glu Gln Arg Ala Leu Asp 130 135 140 Leu Leu Arg Asp Cys Asn Leu Ile Ser Tyr Lys Glu Ala Ser His Leu 145 150 155 160 Asp Ile Thr Ala Lys Asp Val Phe Gly Cys Gly Gly Lys Lys Val Thr 165 170 175 Ile Ile Glu Met Ala Ala Pro Leu Leu Val Ser Ser Leu Pro Asp Val 180 185 190 Asp Ala Ala Val Ile Pro Gly Asn Phe Ala Ile Ala Gly Gly Ile Cys 195 200 205 Pro Tyr Lys Asn Ser Leu Tyr Leu Glu Asp Val Arg Thr Ser Gln Tyr 210 215 220 Thr Asn Val Val Val Ile Arg Ala Glu Asp Met Glu Asp Ser Arg Met 225 230 235 240 His Lys Leu Lys Gln Leu Leu Gln Ser Ser Ser Val Gln Asp Phe Phe 245 250 255 Asn Thr Lys Tyr Lys Gly Ile Phe Leu Ser Gln 260 265 38 402 DNA Chlamydia psittaci 38 catgtatttt acgcaaaaaa taaacggtat aactcctgct tacaagccgc gctataccac 60 aataatatcc cgacaaccgt gtacacaaac cttattgata tcgtgaagaa aaattcttca 120 ctaatcacga agtacttttc catcaaacaa cgatgcttaa atctaaaaga tttccatttt 180 tatgatgttt atgctcccct aagtcagtcc aaagagaaaa aatatacgtt ccaagaagct 240 gtggatctta tctatactag cctttctcct ctaggaacgg aatacattga taccttaaaa 300 caggggttaa caactcaagg ctgggtagat aaatacgaaa atcttaataa acgctccgga 360 gcctattctt cgggatgtta cgatagccac ccttatgtcc tc 402 39 134 PRT Chlamydia psittaci 39 His Val Phe Tyr Ala Lys Asn Lys Arg Tyr Asn Ser Cys Leu Gln Ala 1 5 10 15 Ala Leu Tyr His Asn Asn Ile Pro Thr Thr Val Tyr Thr Asn Leu Ile 20 25 30 Asp Ile Val Lys Lys Asn Ser Ser Leu Ile Thr Lys Tyr Phe Ser Ile 35 40 45 Lys Gln Arg Cys Leu Asn Leu Lys Asp Phe His Phe Tyr Asp Val Tyr 50 55 60 Ala Pro Leu Ser Gln Ser Lys Glu Lys Lys Tyr Thr Phe Gln Glu Ala 65 70 75 80 Val Asp Leu Ile Tyr Thr Ser Leu Ser Pro Leu Gly Thr Glu Tyr Ile 85 90 95 Asp Thr Leu Lys Gln Gly Leu Thr Thr Gln Gly Trp Val Asp Lys Tyr 100 105 110 Glu Asn Leu Asn Lys Arg Ser Gly Ala Tyr Ser Ser Gly Cys Tyr Asp 115 120 125 Ser His Pro Tyr Val Leu 130 40 1827 DNA Chlamydia psittaci 40 atgagcgtag aattcaacaa gcaacaagtc cgtccaagaa gtgaaatttc ccctcaagat 60 tgttgggata tcaccccctt atatctaaat agaaaagcat ggaaagcaga tcttgattct 120 ttcggattaa aaacagacgg ctcacctacg tggcccgctc ttcaagcaac gcaataccaa 180 ctggacaact cagaatctct actatcctta ttaactactc tcttctctat tgagagaaaa 240 ttaaacaaac tctacgttta cgctcatctg actcatgatc aggatattac aaatcaagaa 300 ggcatcgcag atcttaaatc tatcacgcat ctacatacct tatttgccga agaaacctct 360 tgggtacaac ccgctttaac cagcctatcg gaatctctca ttgctcagca cctatcagct 420 ccctgtttag ctccttatag attctattta gagaaaatct ttagactatc tatacacaca 480 ggcactcctg gagaagaaaa aattctcgct tccgccttta ctcctcttga agtagccagt 540 aaggcatttt cttctttaag tgactctgaa attccctttg ggcaagctac agactcagaa 600 ggaaactctc acccgctttc tcatgcactg gcttcattgt atatgcaatc cacagatcgg 660 gaattacgaa aaacatccta cctagcacaa tgtgaaagat atcatagtta ccgacatacc 720 tttgctaact tactcaatgg gaaaatccaa gcccatgtat tttacgcaaa aaataaacgg 780 tataactcct gcttacaagc cgcgctatac cacaataata tcccgacaac cgtgtacaca 840 aaccttattg atatcgtgaa gaaaaattct tcactaatca cgaagtactt ttccatcaaa 900 caacgatgct taaatctaaa agatttccat ttttatgatg tttatgctcc cctaagtcag 960 tccaaagaga aaaaatatac gttccaagaa gctgtggatc ttatctatac tagcctttct 1020 cctctaggaa cggaatacat tgatacctta aaacaggggt taacaactca aggctgggta 1080 gataaatacg aaaatcttaa taaacgctcc ggagcctatt cttcgggatg ttacgatagc 1140 cacccttatg tcctcctaaa ctatacaggc accctgtatg atgtatccgt cattgcccac 1200 gaaggcggac acagtatgca ctcgtatttt agtaggaagc atcaaccttt ccatgacgct 1260 caatatccta ttttccttgc tgaaattgct tctaccttaa atgaaatgct tcttatggat 1320 tccatgctga aggagagcga ctcaaaagaa gagaaaatca ccattctgac acgatgtttg 1380 gataccatct tctctacact attccgtcag gtattattcg cctcttttga atacgatatt 1440 catcacgcag cagaacatgg ggttcctcta actgaagaat acctatcctc aacttacaag 1500 aatttacaaa atgagtttta cggagaaatt atcacatttg atgtcctgtc gaacatagaa 1560 tgggcaagaa ttcctcattt ctattacaat ttctacgtat accaatatgc aacgggcatt 1620 atagccgccc tgtgcttttt agaaaaaatt cttaacaacg aagataacgc tcttaactcc 1680 tatctcaact ttttaaaaag tggtggatca gatttcccct tagaaatctt aaaaaaatca 1740 ggattagata tgggcacagt tgagccaatc caaaaagctt tttgctttat cgagaaaaaa 1800 atccaggagc tatcatcttt aatttga 1827 41 608 PRT Chlamydia psittaci 41 Met Ser Val Glu Phe Asn Lys Gln Gln Val Arg Pro Arg Ser Glu Ile 1 5 10 15 Ser Pro Gln Asp Cys Trp Asp Ile Thr Pro Leu Tyr Leu Asn Arg Lys 20 25 30 Ala Trp Lys Ala Asp Leu Asp Ser Phe Gly Leu Lys Thr Asp Gly Ser 35 40 45 Pro Thr Trp Pro Ala Leu Gln Ala Thr Gln Tyr Gln Leu Asp Asn Ser 50 55 60 Glu Ser Leu Leu Ser Leu Leu Thr Thr Leu Phe Ser Ile Glu Arg Lys 65 70 75 80 Leu Asn Lys Leu Tyr Val Tyr Ala His Leu Thr His Asp Gln Asp Ile 85 90 95 Thr Asn Gln Glu Gly Ile Ala Asp Leu Lys Ser Ile Thr His Leu His 100 105 110 Thr Leu Phe Ala Glu Glu Thr Ser Trp Val Gln Pro Ala Leu Thr Ser 115 120 125 Leu Ser Glu Ser Leu Ile Ala Gln His Leu Ser Ala Pro Cys Leu Ala 130 135 140 Pro Tyr Arg Phe Tyr Leu Glu Lys Ile Phe Arg Leu Ser Ile His Thr 145 150 155 160 Gly Thr Pro Gly Glu Glu Lys Ile Leu Ala Ser Ala Phe Thr Pro Leu 165 170 175 Glu Val Ala Ser Lys Ala Phe Ser Ser Leu Ser Asp Ser Glu Ile Pro 180 185 190 Phe Gly Gln Ala Thr Asp Ser Glu Gly Asn Ser His Pro Leu Ser His 195 200 205 Ala Leu Ala Ser Leu Tyr Met Gln Ser Thr Asp Arg Glu Leu Arg Lys 210 215 220 Thr Ser Tyr Leu Ala Gln Cys Glu Arg Tyr His Ser Tyr Arg His Thr 225 230 235 240 Phe Ala Asn Leu Leu Asn Gly Lys Ile Gln Ala His Val Phe Tyr Ala 245 250 255 Lys Asn Lys Arg Tyr Asn Ser Cys Leu Gln Ala Ala Leu Tyr His Asn 260 265 270 Asn Ile Pro Thr Thr Val Tyr Thr Asn Leu Ile Asp Ile Val Lys Lys 275 280 285 Asn Ser Ser Leu Ile Thr Lys Tyr Phe Ser Ile Lys Gln Arg Cys Leu 290 295 300 Asn Leu Lys Asp Phe His Phe Tyr Asp Val Tyr Ala Pro Leu Ser Gln 305 310 315 320 Ser Lys Glu Lys Lys Tyr Thr Phe Gln Glu Ala Val Asp Leu Ile Tyr 325 330 335 Thr Ser Leu Ser Pro Leu Gly Thr Glu Tyr Ile Asp Thr Leu Lys Gln 340 345 350 Gly Leu Thr Thr Gln Gly Trp Val Asp Lys Tyr Glu Asn Leu Asn Lys 355 360 365 Arg Ser Gly Ala Tyr Ser Ser Gly Cys Tyr Asp Ser His Pro Tyr Val 370 375 380 Leu Leu Asn Tyr Thr Gly Thr Leu Tyr Asp Val Ser Val Ile Ala His 385 390 395 400 Glu Gly Gly His Ser Met His Ser Tyr Phe Ser Arg Lys His Gln Pro 405 410 415 Phe His Asp Ala Gln Tyr Pro Ile Phe Leu Ala Glu Ile Ala Ser Thr 420 425 430 Leu Asn Glu Met Leu Leu Met Asp Ser Met Leu Lys Glu Ser Asp Ser 435 440 445 Lys Glu Glu Lys Ile Thr Ile Leu Thr Arg Cys Leu Asp Thr Ile Phe 450 455 460 Ser Thr Leu Phe Arg Gln Val Leu Phe Ala Ser Phe Glu Tyr Asp Ile 465 470 475 480 His His Ala Ala Glu His Gly Val Pro Leu Thr Glu Glu Tyr Leu Ser 485 490 495 Ser Thr Tyr Lys Asn Leu Gln Asn Glu Phe Tyr Gly Glu Ile Ile Thr 500 505 510 Phe Asp Val Leu Ser Asn Ile Glu Trp Ala Arg Ile Pro His Phe Tyr 515 520 525 Tyr Asn Phe Tyr Val Tyr Gln Tyr Ala Thr Gly Ile Ile Ala Ala Leu 530 535 540 Cys Phe Leu Glu Lys Ile Leu Asn Asn Glu Asp Asn Ala Leu Asn Ser 545 550 555 560 Tyr Leu Asn Phe Leu Lys Ser Gly Gly Ser Asp Phe Pro Leu Glu Ile 565 570 575 Leu Lys Lys Ser Gly Leu Asp Met Gly Thr Val Glu Pro Ile Gln Lys 580 585 590 Ala Phe Cys Phe Ile Glu Lys Lys Ile Gln Glu Leu Ser Ser Leu Ile 595 600 605 42 1517 DNA Chlamydia psittaci 42 gcgttagatt cggaagagct gaaagagcaa ataaacaatc taaaagagcg tttatgggat 60 gcacaatcca ctctacaaca agatcaaaat aaactatcgc aagaacattt tgaagctgtc 120 agtgtgatca ttgatttaat caatggtgat ctgaatgata tagctgagca tacgcaacaa 180 aacttacaaa ccaaaaaaga agaagaacac gagtccgttg cccgtaagat ggtcaattgg 240 gtgtcttctg gagaagaagt gttaaataga gcccttctct acttctcaga taggaatgga 300 gaacgggaaa atttagcaga ctttttaaaa gtacagtatg ctgttcaaag agcaacgcaa 360 agagcagaac tttttgctag tatcgtagga actacggtaa gtagtataaa gacgataatg 420 accacacaat taggttaaca tggacgaatt gacgacagat ttcgataccc tcatgtcgca 480 attgaacgac gtacacttga ctaccgttgt cggtcgtata actgaagtcg tcggtatgtt 540 aattaaagct gtcgttccca atgtacgcgt tggggaggta tgcttagtta aacgttatgg 600 tatggagccg ctcgtgaccg aagtcgtcgg cttcacacaa aatttcgctt ttttatcgcc 660 actaggagaa cttactggag tcagcccttc ttcagaggtt attcccacag gtctgccttt 720 gtatatccgt gcaggtaacg gtcttttagg tcgtgtattg aatggtctgg gagaacctat 780 cgactccgag atcaaaggac ctttggttga tgttaacgaa acctaccctg tgtttcgcgc 840 tccaccagat ccattgcata gagaaaaatt aagaacaatt ttatccaccg gcgtgcggtg 900 tatcgacggt atgctcacag tcgccagagg ccagcgtata ggcatttttg ctggagctgg 960 ggtgggtaaa tcgtctctct tgggaatgat cgctagaaac gcggaagaag ccgatgtcaa 1020 tgtgattgct ctcatcggag agcggggccg agaggttcgt gaatttatcg agggcgatct 1080 cggagaagaa ggaatgaaac gttcggtgat cgtcgtctct acttcagatc aatcctcaca 1140 gttgcgatta aatgctgctt acgtaggcac cgctatagca gagtattttc gtgatcaggg 1200 caaaaccgta gttttgatga tggattctgt cacccgattt gcccgagccc taagagaagt 1260 cggtctagct gccggagaac cgccagctcg aggaggatac acaccttctg tattctcaac 1320 tttgcctagg ttattagaac gttccggagc ttcggataaa ggaacaatca cagcctttta 1380 cacagtactt gttgccgggg atgatatgaa tgaaccggtc gctgatgaag ttaaatcgat 1440 tcttgatggt cacgttgtct tgtctaacgc tttagctcag gcataccatt atcctgctat 1500 tgatgtctta gcatcta 1517 43 145 PRT Chlamydia psittaci 43 Ala Leu Asp Ser Glu Glu Leu Lys Glu Gln Ile Asn Asn Leu Lys Glu 1 5 10 15 Arg Leu Trp Asp Ala Gln Ser Thr Leu Gln Gln Asp Gln Asn Lys Leu 20 25 30 Ser Gln Glu His Phe Glu Ala Val Ser Val Ile Ile Asp Leu Ile Asn 35 40 45 Gly Asp Leu Asn Asp Ile Ala Glu His Thr Gln Gln Asn Leu Gln Thr 50 55 60 Lys Lys Glu Glu Glu His Glu Ser Val Ala Arg Lys Met Val Asn Trp 65 70 75 80 Val Ser Ser Gly Glu Glu Val Leu Asn Arg Ala Leu Leu Tyr Phe Ser 85 90 95 Asp Arg Asn Gly Glu Arg Glu Asn Leu Ala Asp Phe Leu Lys Val Gln 100 105 110 Tyr Ala Val Gln Arg Ala Thr Gln Arg Ala Glu Leu Phe Ala Ser Ile 115 120 125 Val Gly Thr Thr Val Ser Ser Ile Lys Thr Ile Met Thr Thr Gln Leu 130 135 140 Gly 145 44 669 DNA Chlamydia psittaci 44 atggtagatc ctttgaagct tttcccaaag ctagactccg agaaagaaac agcttctata 60 cagaagcctt taggaactcc tttagccagt gagttacata aggaagttcc tgcattttct 120 ttagggacgg cagcagactc cttgaataaa aatatagagg atgtcaagcc taaccctatg 180 gcgatgatgc aagacagaaa ctctaacatt atcgatcctg aactggaaga ggcgttagat 240 tcggaagagc tgaaagagca aataaacaat ctaaaagagc gtttatggga tgcacaatcc 300 actctacaac aagatcaaaa taaactatcg caagaacatt ttgaagctgt cagtgtgatc 360 attgatttaa tcaatggtga tctgaatgat atagctgagc atacgcaaca aaacttacaa 420 accaaaaaag aagaagaaca cgagtccgtt gcccgtaaga tggtcaattg ggtgtcttct 480 ggagaagaag tgttaaatag agcccttctc tacttctcag ataggaatgg agaacgggaa 540 aatttagcag actttttaaa agtacagtat gctgttcaaa gagcaacgca aagagcagaa 600 ctttttgcta gtatcgtagg aactacggta agtagtataa agacgataat gaccacacaa 660 ttaggttaa 669 45 222 PRT Chlamydia psittaci 45 Met Val Asp Pro Leu Lys Leu Phe Pro Lys Leu Asp Ser Glu Lys Glu 1 5 10 15 Thr Ala Ser Ile Gln Lys Pro Leu Gly Thr Pro Leu Ala Ser Glu Leu 20 25 30 His Lys Glu Val Pro Ala Phe Ser Leu Gly Thr Ala Ala Asp Ser Leu 35 40 45 Asn Lys Asn Ile Glu Asp Val Lys Pro Asn Pro Met Ala Met Met Gln 50 55 60 Asp Arg Asn Ser Asn Ile Ile Asp Pro Glu Leu Glu Glu Ala Leu Asp 65 70 75 80 Ser Glu Glu Leu Lys Glu Gln Ile Asn Asn Leu Lys Glu Arg Leu Trp 85 90 95 Asp Ala Gln Ser Thr Leu Gln Gln Asp Gln Asn Lys Leu Ser Gln Glu 100 105 110 His Phe Glu Ala Val Ser Val Ile Ile Asp Leu Ile Asn Gly Asp Leu 115 120 125 Asn Asp Ile Ala Glu His Thr Gln Gln Asn Leu Gln Thr Lys Lys Glu 130 135 140 Glu Glu His Glu Ser Val Ala Arg Lys Met Val Asn Trp Val Ser Ser 145 150 155 160 Gly Glu Glu Val Leu Asn Arg Ala Leu Leu Tyr Phe Ser Asp Arg Asn 165 170 175 Gly Glu Arg Glu Asn Leu Ala Asp Phe Leu Lys Val Gln Tyr Ala Val 180 185 190 Gln Arg Ala Thr Gln Arg Ala Glu Leu Phe Ala Ser Ile Val Gly Thr 195 200 205 Thr Val Ser Ser Ile Lys Thr Ile Met Thr Thr Gln Leu Gly 210 215 220 46 1329 DNA Chlamydia psittaci 46 atggacgaat tgacgacaga tttcgatacc ctcatgtcgc aattgaacga cgtacacttg 60 actaccgttg tcggtcgtat aactgaagtc gtcggtatgt taattaaagc tgtcgttccc 120 aatgtacgcg ttggggaggt atgcttagtt aaacgttatg gtatggagcc gctcgtgacc 180 gaagtcgtcg gcttcacaca aaatttcgct tttttatcgc cactaggaga acttactgga 240 gtcagccctt cttcagaggt tattcccaca ggtctgcctt tgtatatccg tgcaggtaac 300 ggtcttttag gtcgtgtatt gaatggtctg ggagaaccta tcgactccga gatcaaagga 360 cctttggttg atgttaacga aacctaccct gtgtttcgcg ctccaccaga tccattgcat 420 agagaaaaat taagaacaat tttatccacc ggcgtgcggt gtatcgacgg tatgctcaca 480 gtcgccagag gccagcgtat aggcattttt gctggagctg gggtgggtaa atcgtctctc 540 ttgggaatga tcgctagaaa cgcggaagaa gccgatgtca atgtgattgc tctcatcgga 600 gagcggggcc gagaggttcg tgaatttatc gagggcgatc tcggagaaga aggaatgaaa 660 cgttcggtga tcgtcgtctc tacttcagat caatcctcac agttgcgatt aaatgctgct 720 tacgtaggca ccgctatagc agagtatttt cgtgatcagg gcaaaaccgt agttttgatg 780 atggattctg tcacccgatt tgcccgagcc ctaagagaag tcggtctagc tgccggagaa 840 ccgccagctc gaggaggata cacaccttct gtattctcaa ctttgcctag gttattagaa 900 cgttccggag cttcggataa aggaacaatc acagcctttt acacagtact tgttgccggg 960 gatgatatga atgaaccggt cgctgatgaa gttaaatcga ttcttgatgg tcacgttgtc 1020 ttgtctaacg ctttagctca ggcataccat tatcctgcta ttgatgtctt agcatctatc 1080 agccgattgc tgacagcaat tgttcctgag gaacaacgac gcatcatagg aaaagcccga 1140 gaggtgctgg caaaatacaa agcaaacgaa atgcttatac gtattggaga atatcgccga 1200 gggtccgatc gtgaagtgga ttttgctata gatcacattg ataaattgaa cagattctta 1260 aagcaagata ttcatgaaaa aacaaattac gaggaagcct cgcaacagct tcgggctatt 1320 ttccgataa 1329 47 442 PRT Chlamydia psittaci 47 Met Asp Glu Leu Thr Thr Asp Phe Asp Thr Leu Met Ser Gln Leu Asn 1 5 10 15 Asp Val His Leu Thr Thr Val Val Gly Arg Ile Thr Glu Val Val Gly 20 25 30 Met Leu Ile Lys Ala Val Val Pro Asn Val Arg Val Gly Glu Val Cys 35 40 45 Leu Val Lys Arg Tyr Gly Met Glu Pro Leu Val Thr Glu Val Val Gly 50 55 60 Phe Thr Gln Asn Phe Ala Phe Leu Ser Pro Leu Gly Glu Leu Thr Gly 65 70 75 80 Val Ser Pro Ser Ser Glu Val Ile Pro Thr Gly Leu Pro Leu Tyr Ile 85 90 95 Arg Ala Gly Asn Gly Leu Leu Gly Arg Val Leu Asn Gly Leu Gly Glu 100 105 110 Pro Ile Asp Ser Glu Ile Lys Gly Pro Leu Val Asp Val Asn Glu Thr 115 120 125 Tyr Pro Val Phe Arg Ala Pro Pro Asp Pro Leu His Arg Glu Lys Leu 130 135 140 Arg Thr Ile Leu Ser Thr Gly Val Arg Cys Ile Asp Gly Met Leu Thr 145 150 155 160 Val Ala Arg Gly Gln Arg Ile Gly Ile Phe Ala Gly Ala Gly Val Gly 165 170 175 Lys Ser Ser Leu Leu Gly Met Ile Ala Arg Asn Ala Glu Glu Ala Asp 180 185 190 Val Asn Val Ile Ala Leu Ile Gly Glu Arg Gly Arg Glu Val Arg Glu 195 200 205 Phe Ile Glu Gly Asp Leu Gly Glu Glu Gly Met Lys Arg Ser Val Ile 210 215 220 Val Val Ser Thr Ser Asp Gln Ser Ser Gln Leu Arg Leu Asn Ala Ala 225 230 235 240 Tyr Val Gly Thr Ala Ile Ala Glu Tyr Phe Arg Asp Gln Gly Lys Thr 245 250 255 Val Val Leu Met Met Asp Ser Val Thr Arg Phe Ala Arg Ala Leu Arg 260 265 270 Glu Val Gly Leu Ala Ala Gly Glu Pro Pro Ala Arg Gly Gly Tyr Thr 275 280 285 Pro Ser Val Phe Ser Thr Leu Pro Arg Leu Leu Glu Arg Ser Gly Ala 290 295 300 Ser Asp Lys Gly Thr Ile Thr Ala Phe Tyr Thr Val Leu Val Ala Gly 305 310 315 320 Asp Asp Met Asn Glu Pro Val Ala Asp Glu Val Lys Ser Ile Leu Asp 325 330 335 Gly His Val Val Leu Ser Asn Ala Leu Ala Gln Ala Tyr His Tyr Pro 340 345 350 Ala Ile Asp Val Leu Ala Ser Ile Ser Arg Leu Leu Thr Ala Ile Val 355 360 365 Pro Glu Glu Gln Arg Arg Ile Ile Gly Lys Ala Arg Glu Val Leu Ala 370 375 380 Lys Tyr Lys Ala Asn Glu Met Leu Ile Arg Ile Gly Glu Tyr Arg Arg 385 390 395 400 Gly Ser Asp Arg Glu Val Asp Phe Ala Ile Asp His Ile Asp Lys Leu 405 410 415 Asn Arg Phe Leu Lys Gln Asp Ile His Glu Lys Thr Asn Tyr Glu Glu 420 425 430 Ala Ser Gln Gln Leu Arg Ala Ile Phe Arg 435 440 48 477 DNA Chlamydia psittaci 48 cttcttgcag atgccgactc tgtcaacctt gcaactggat tcaacggctc cactagtgaa 60 actttcaatg ttaaacaaac agataatgct gacgggacaa catatattct aggcagcgcg 120 atcacctttg aacacataaa tcaattaaaa ccagcaaaca ctagctgttt tgctaataca 180 gctggagatc taacgtttac tgggaatcga cgacttctct atttcaataa tatttcatca 240 acagcgaaag gtgccgctat cagcacaact gcggatggta agacactcac aatatccggg 300 gctctacaac tgattttcta catgtcgcca agattggcca cgggaaatgg cgtcatttat 360 tctaatagct ctgtactcat cgagaacaat tctcaaggta gctcgggact gaataagtct 420 gcagggaaag gcgtctttat ttgttgtgag aaaagtacgg atgtgggagc tacatca 477 49 159 PRT Chlamydia psittaci 49 Leu Leu Ala Asp Ala Asp Ser Val Asn Leu Ala Thr Gly Phe Asn Gly 1 5 10 15 Ser Thr Ser Glu Thr Phe Asn Val Lys Gln Thr Asp Asn Ala Asp Gly 20 25 30 Thr Thr Tyr Ile Leu Gly Ser Ala Ile Thr Phe Glu His Ile Asn Gln 35 40 45 Leu Lys Pro Ala Asn Thr Ser Cys Phe Ala Asn Thr Ala Gly Asp Leu 50 55 60 Thr Phe Thr Gly Asn Arg Arg Leu Leu Tyr Phe Asn Asn Ile Ser Ser 65 70 75 80 Thr Ala Lys Gly Ala Ala Ile Ser Thr Thr Ala Asp Gly Lys Thr Leu 85 90 95 Thr Ile Ser Gly Ala Leu Gln Leu Ile Phe Tyr Met Ser Pro Arg Leu 100 105 110 Ala Thr Gly Asn Gly Val Ile Tyr Ser Asn Ser Ser Val Leu Ile Glu 115 120 125 Asn Asn Ser Gln Gly Ser Ser Gly Leu Asn Lys Ser Ala Gly Lys Gly 130 135 140 Val Phe Ile Cys Cys Glu Lys Ser Thr Asp Val Gly Ala Thr Ser 145 150 155 50 591 DNA Chlamydia psittaci 50 acctttgaac acataaatca attaaaacca gcaaacacta gctgttttgc taatacagct 60 ggagatctaa cgtttactgg gaatcgacga cttctctatt tcaataatat ttcatcaaca 120 gcgaaaggtg ccgctatcag cacaactgcg gatggtaaga cactcacaat atccggggct 180 ctacaactga ttttctacat gtcgccaaga ttggccacgg gaaatggcgt catttattct 240 aatagctctg tactcatcga gaacaattct caaggtagct cgggactgaa taagtctgca 300 gggaaaggcg tctttatttg ttgtgagaaa agtacggatg tgggagctac atcaccgaca 360 ttaatcatac ggaataacgg agagtttctt actgtaggta atgcagctac tagctctgga 420 ggagcgattt atgcggagaa aatgatctta tcctcaggag gatatacaaa atttcaatcc 480 aatgttagct atgatcaagg tggggccatt gccattgctc ctaatggaga aattagtctc 540 tccgcggata aaggaaatat cgtctttgaa agaaacctta aaattgccaa c 591 51 197 PRT Chlamydia psittaci 51 Thr Phe Glu His Ile Asn Gln Leu Lys Pro Ala Asn Thr Ser Cys Phe 1 5 10 15 Ala Asn Thr Ala Gly Asp Leu Thr Phe Thr Gly Asn Arg Arg Leu Leu 20 25 30 Tyr Phe Asn Asn Ile Ser Ser Thr Ala Lys Gly Ala Ala Ile Ser Thr 35 40 45 Thr Ala Asp Gly Lys Thr Leu Thr Ile Ser Gly Ala Leu Gln Leu Ile 50 55 60 Phe Tyr Met Ser Pro Arg Leu Ala Thr Gly Asn Gly Val Ile Tyr Ser 65 70 75 80 Asn Ser Ser Val Leu Ile Glu Asn Asn Ser Gln Gly Ser Ser Gly Leu 85 90 95 Asn Lys Ser Ala Gly Lys Gly Val Phe Ile Cys Cys Glu Lys Ser Thr 100 105 110 Asp Val Gly Ala Thr Ser Pro Thr Leu Ile Ile Arg Asn Asn Gly Glu 115 120 125 Phe Leu Thr Val Gly Asn Ala Ala Thr Ser Ser Gly Gly Ala Ile Tyr 130 135 140 Ala Glu Lys Met Ile Leu Ser Ser Gly Gly Tyr Thr Lys Phe Gln Ser 145 150 155 160 Asn Val Ser Tyr Asp Gln Gly Gly Ala Ile Ala Ile Ala Pro Asn Gly 165 170 175 Glu Ile Ser Leu Ser Ala Asp Lys Gly Asn Ile Val Phe Glu Arg Asn 180 185 190 Leu Lys Ile Ala Asn 195 52 2040 DNA Chlamydia psittaci 52 atgcagggaa tactaatgaa aaactctatt tatggggttt tactgttttc ctcttttgcc 60 ttatccactg ctaccaaact tcttgcagat gccgactctg tcaaccttgc aactggattc 120 aacggctcca ctagtgaaac tttcaatgtt aaacaaacag ataatgctga cgggacaaca 180 tatattctag gcagcgcgat cacctttgaa cacataaatc aattaaaacc agcaaacact 240 agctgttttg ctaatacagc tggagatcta acgtttactg ggaatcgacg acttctctat 300 ttcaataata tttcatcaac agcgaaaggt gccgctatca gcacaactgc ggatggtaag 360 acactcacaa tatccggggc tctacaactg attttctaca tgtcgccaag attggccacg 420 ggaaatggcg tcatttattc taatagctct gtactcatcg agaacaattc tcaaggtagc 480 tcgggactga ataagtctgc agggaaaggc gtctttattt gttgtgagaa aagtacggat 540 gtgggagcta catcaccgac attaatcata cggaataacg gagagtttct tactgtaggt 600 aatgcagcta ctagctctgg aggagcgatt tatgcggaga aaatgatctt atcctcagga 660 ggatatacaa aatttcaatc caatgttagc tatgatcaag gtggggccat tgccattgct 720 cctaatggag aaattagtct ctccgcggat aaaggaaata tcgtctttga aagaaacctt 780 aaaattgcca acaaacaaaa tactcccaat gccattcacc taggagacaa tgcgaaattt 840 cttcaattac gtgctgctaa caacaaagcc atattttttt atgacccgat tacaaccacg 900 ggatctgtgg cagatcggct aattattaat aactcgcaag gagaagcctc gacttacgat 960 ggggcgattg tattttctag tctcaactta ttcactcatt cccctgaatg taaactctct 1020 tcattttctc aaggtcttac tttagcggca ggatcattag ttttagaaga gggggtatgt 1080 gtacaagctc cgtcttttga tcaacgtgct cactcccaac tattcatgaa tcctgggacg 1140 aagttacaag ctacccagaa catctcggta aagaatctcc atctcaatct taatagaata 1200 gcagaagagc cggcgtatat caccacaaca gacgatgctt ctagtgtgga catttgcgga 1260 cctgtagtta tgcatataga tgatgagatc ttctataatc agacagtatt agcaaatgag 1320 ttgtctgtag agtgtttaaa tctcagttct ccacatctcg ataatatcac tattgatgac 1380 gttcccgcag tgcctatcat gacgttagaa tcgcatcgtg gttatcaagg tacatgggaa 1440 atctcttgga aagagcaacc taaacttacc tttgggaagg cgactatcgc gcctaataag 1500 cagatgcacc ttatttggaa accttctggt tacgttcctt tctcaggggg aactggagag 1560 tttacgacat ctttagtgcc taatagctta tggaatctct ttttagatac acgtttttct 1620 caacaagcga ttgagaaaca tgctgtatct tcaggtaacg gtatatggat ttcctccatg 1680 accaattctt ttcttcaagg ttctacgaac aacaaccacg gctttcgtca taagagttca 1740 ggatataccg cagggggaaa aatacaaaca cttcaagatg atatctttag tgtcagtttt 1800 tctcagctat ttgggagatc taaggatttt ggatctgcca catctaagga tacattccta 1860 tcgggctcta tctatgctca gcattcgaga cgcttacttc ctataatgag attccttgca 1920 ggaacatcaa catatagacc gcgactctta ctgagtattc ccaagaatct tcctatcaat 1980 tttgatgttc ttgtgagtta cagctatgac agtaaccaca tgaaagtaca aaaattctaa 2040 53 679 PRT Chlamydia psittaci 53 Met Gln Gly Ile Leu Met Lys Asn Ser Ile Tyr Gly Val Leu Leu Phe 1 5 10 15 Ser Ser Phe Ala Leu Ser Thr Ala Thr Lys Leu Leu Ala Asp Ala Asp 20 25 30 Ser Val Asn Leu Ala Thr Gly Phe Asn Gly Ser Thr Ser Glu Thr Phe 35 40 45 Asn Val Lys Gln Thr Asp Asn Ala Asp Gly Thr Thr Tyr Ile Leu Gly 50 55 60 Ser Ala Ile Thr Phe Glu His Ile Asn Gln Leu Lys Pro Ala Asn Thr 65 70 75 80 Ser Cys Phe Ala Asn Thr Ala Gly Asp Leu Thr Phe Thr Gly Asn Arg 85 90 95 Arg Leu Leu Tyr Phe Asn Asn Ile Ser Ser Thr Ala Lys Gly Ala Ala 100 105 110 Ile Ser Thr Thr Ala Asp Gly Lys Thr Leu Thr Ile Ser Gly Ala Leu 115 120 125 Gln Leu Ile Phe Tyr Met Ser Pro Arg Leu Ala Thr Gly Asn Gly Val 130 135 140 Ile Tyr Ser Asn Ser Ser Val Leu Ile Glu Asn Asn Ser Gln Gly Ser 145 150 155 160 Ser Gly Leu Asn Lys Ser Ala Gly Lys Gly Val Phe Ile Cys Cys Glu 165 170 175 Lys Ser Thr Asp Val Gly Ala Thr Ser Pro Thr Leu Ile Ile Arg Asn 180 185 190 Asn Gly Glu Phe Leu Thr Val Gly Asn Ala Ala Thr Ser Ser Gly Gly 195 200 205 Ala Ile Tyr Ala Glu Lys Met Ile Leu Ser Ser Gly Gly Tyr Thr Lys 210 215 220 Phe Gln Ser Asn Val Ser Tyr Asp Gln Gly Gly Ala Ile Ala Ile Ala 225 230 235 240 Pro Asn Gly Glu Ile Ser Leu Ser Ala Asp Lys Gly Asn Ile Val Phe 245 250 255 Glu Arg Asn Leu Lys Ile Ala Asn Lys Gln Asn Thr Pro Asn Ala Ile 260 265 270 His Leu Gly Asp Asn Ala Lys Phe Leu Gln Leu Arg Ala Ala Asn Asn 275 280 285 Lys Ala Ile Phe Phe Tyr Asp Pro Ile Thr Thr Thr Gly Ser Val Ala 290 295 300 Asp Arg Leu Ile Ile Asn Asn Ser Gln Gly Glu Ala Ser Thr Tyr Asp 305 310 315 320 Gly Ala Ile Val Phe Ser Ser Leu Asn Leu Phe Thr His Ser Pro Glu 325 330 335 Cys Lys Leu Ser Ser Phe Ser Gln Gly Leu Thr Leu Ala Ala Gly Ser 340 345 350 Leu Val Leu Glu Glu Gly Val Cys Val Gln Ala Pro Ser Phe Asp Gln 355 360 365 Arg Ala His Ser Gln Leu Phe Met Asn Pro Gly Thr Lys Leu Gln Ala 370 375 380 Thr Gln Asn Ile Ser Val Lys Asn Leu His Leu Asn Leu Asn Arg Ile 385 390 395 400 Ala Glu Glu Pro Ala Tyr Ile Thr Thr Thr Asp Asp Ala Ser Ser Val 405 410 415 Asp Ile Cys Gly Pro Val Val Met His Ile Asp Asp Glu Ile Phe Tyr 420 425 430 Asn Gln Thr Val Leu Ala Asn Glu Leu Ser Val Glu Cys Leu Asn Leu 435 440 445 Ser Ser Pro His Leu Asp Asn Ile Thr Ile Asp Asp Val Pro Ala Val 450 455 460 Pro Ile Met Thr Leu Glu Ser His Arg Gly Tyr Gln Gly Thr Trp Glu 465 470 475 480 Ile Ser Trp Lys Glu Gln Pro Lys Leu Thr Phe Gly Lys Ala Thr Ile 485 490 495 Ala Pro Asn Lys Gln Met His Leu Ile Trp Lys Pro Ser Gly Tyr Val 500 505 510 Pro Phe Ser Gly Gly Thr Gly Glu Phe Thr Thr Ser Leu Val Pro Asn 515 520 525 Ser Leu Trp Asn Leu Phe Leu Asp Thr Arg Phe Ser Gln Gln Ala Ile 530 535 540 Glu Lys His Ala Val Ser Ser Gly Asn Gly Ile Trp Ile Ser Ser Met 545 550 555 560 Thr Asn Ser Phe Leu Gln Gly Ser Thr Asn Asn Asn His Gly Phe Arg 565 570 575 His Lys Ser Ser Gly Tyr Thr Ala Gly Gly Lys Ile Gln Thr Leu Gln 580 585 590 Asp Asp Ile Phe Ser Val Ser Phe Ser Gln Leu Phe Gly Arg Ser Lys 595 600 605 Asp Phe Gly Ser Ala Thr Ser Lys Asp Thr Phe Leu Ser Gly Ser Ile 610 615 620 Tyr Ala Gln His Ser Arg Arg Leu Leu Pro Ile Met Arg Phe Leu Ala 625 630 635 640 Gly Thr Ser Thr Tyr Arg Pro Arg Leu Leu Leu Ser Ile Pro Lys Asn 645 650 655 Leu Pro Ile Asn Phe Asp Val Leu Val Ser Tyr Ser Tyr Asp Ser Asn 660 665 670 His Met Lys Val Gln Lys Phe 675 54 487 DNA Chlamydia psittaci 54 acctcgagag aggattctct tagtgtggct ttctgtcagt tatttgcaaa agataaagac 60 taccttgtaa gcaagaacgc cgcaaacgtc tatgcgggtt ctgtatatta tcagcatgtg 120 agcaagtttg atgatctcac gcggttattt aatgggccta acacgtgttg ttcagggttt 180 tctaaagaga ttcctatttt cttggatgca caaattacct attgccacac ggccaacaac 240 atgacaacgt cctatacaga ctatcctgaa gtgaaaggtt cttggggtaa tgataccctg 300 ggcttaactt tgtctactag cgtacctatc ccggtattta gttcttctat ctttgatagt 360 tatgcaccgt ttgcaaaatt acaagttgtc tatgcgcacc aagatgactt taaagaacca 420 acaacagaag gccgggtctt tgaaagcagc gatcttctca acgtttctgt acctataggt 480 ataaaat 487 55 162 PRT Chlamydia psittaci 55 Thr Ser Arg Glu Asp Ser Leu Ser Val Ala Phe Cys Gln Leu Phe Ala 1 5 10 15 Lys Asp Lys Asp Tyr Leu Val Ser Lys Asn Ala Ala Asn Val Tyr Ala 20 25 30 Gly Ser Val Tyr Tyr Gln His Val Ser Lys Phe Asp Asp Leu Thr Arg 35 40 45 Leu Phe Asn Gly Pro Asn Thr Cys Cys Ser Gly Phe Ser Lys Glu Ile 50 55 60 Pro Ile Phe Leu Asp Ala Gln Ile Thr Tyr Cys His Thr Ala Asn Asn 65 70 75 80 Met Thr Thr Ser Tyr Thr Asp Tyr Pro Glu Val Lys Gly Ser Trp Gly 85 90 95 Asn Asp Thr Leu Gly Leu Thr Leu Ser Thr Ser Val Pro Ile Pro Val 100 105 110 Phe Ser Ser Ser Ile Phe Asp Ser Tyr Ala Pro Phe Ala Lys Leu Gln 115 120 125 Val Val Tyr Ala His Gln Asp Asp Phe Lys Glu Pro Thr Thr Glu Gly 130 135 140 Arg Val Phe Glu Ser Ser Asp Leu Leu Asn Val Ser Val Pro Ile Gly 145 150 155 160 Ile Lys 56 2781 DNA Chlamydia psittaci 56 atgaggcctt ctttatataa gattttaata tcgtcgacgc tgacgttacc aatatctttt 60 cacttctcgc aattgcatgc agaagtggct ttaactcaag aatctattct cgatgcaaat 120 ggagcattca gtccgcaatc tacaagcact gcgggaggaa cgatttacaa cgtcgagagt 180 gatatttcta ttgtagatgt aggacagaca gcggctcttg cttcctcagc ttttgttcag 240 actgcagaca acctaacttt caaagggaac aaccatagct tatccataac gaacgcgaat 300 gccggagcta atcctgcggg aattaacgtt aacactgccg ataagattct tacgctgaca 360 gatttttcta agttgagctt taaggaatgc ccatcttctc tagtgaatac tggaaaaggg 420 gctatgaaat ccggaggagc attaaactta gcgaataatg ccagtattct gtttgatcag 480 aactattccg ctgagaatgg tggagccatc tcttgcaaag ctttttctct aaccggctcg 540 agcaaagaaa tcagcttcac cactaactct actgcgaaaa aaggtggagc gattgctgct 600 acgggaatag ctcatctttc ggacaaccaa ggcacaatca gattttctgg gaacactgct 660 gtgaattctg ggggagcagt atattcagaa gcttctatga cgattgcagg taacaaccac 720 gttgctttta gcaacaatgc tgtttccggt tcatctgatg gttgcggtgg agctatccat 780 tgtagcaaaa caggttcagc accgaccctt actataagag ataacaaagt cttgattttt 840 gaggaaaata cttcttcagc aaaaggtgga gcgatttaca ccgataaact catattgact 900 tctggtgggc ctacggcatt tatcaataac aaagttaccc atgctacacc taagggtgga 960 gctattggta ttgctgccaa tggagaatgt agcttaaccg ctgaacatgg ggatattact 1020 tttgataata acctgatggc cacacaagac aatgctacaa taaaaagaaa tgccattaac 1080 attgaaggca atggtaaatt cgtcaactta cgtgcagcgt ctggaaagac gatttctttc 1140 tatgatccta tcacagttga aggtaatgct gctgatcttc tcactttgaa taaagctgag 1200 ggtgataaaa cgtataatgg aagaattatt ttttcaggag aaaagctcac tgaagaacaa 1260 gctgctgttg cggataacct aaagacaaca tttacacagc ctatcacttt agctgctggt 1320 gaacttgtgt tacgcagcgg tgtggaagta gaagcaaaaa cagtcgtgca aacagcagga 1380 tctttgattc tgatggatgc aggcacaaag ttatccgcaa aaacagaaga tgctacactg 1440 acgaatctgg ctattaatcc gaatacctta gatgggaaaa aattcgccgt agtcgatgcc 1500 gttgctgctg ggaagaatgt gactttatca ggtgctattg gcgttattga tcctacaggg 1560 aagttttatg aaaaccataa gctaaatgat acgttagctt taggaggaat tcaactttct 1620 gggaaaggtt cggtgacaac aaccaacgtg cctagtcatg ttgttggtgt tgctgaaacc 1680 cactatggtt atcaaggaaa ctggtctgtc agttgggtca aagataataa ctctgatcct 1740 aaaacacaaa cagcaatctt tacctggaat aaaacaggat atgttccaaa tcctgaacgt 1800 cgtgctccgc tagtactcaa tagcctttgg ggatccttta tagatttacg ttctattcaa 1860 gatgtcttgg aacgtagtgt tgatagtatt cttgagacac gtcgtggttt gtgggtctct 1920 ggaattggga acttcttcca taaagatcgg aatgctgaaa atcgcaaatt ccgtcatatc 1980 agttcgggat atgtgttagg agccacaaca aatacctcga gagaggattc tcttagtgtg 2040 gctttctgtc agttatttgc aaaagataaa gactaccttg taagcaagaa cgccgcaaac 2100 gtctatgcgg gttctgtata ttatcagcat gtgagcaagt ttgatgatct cacgcggtta 2160 tttaatgggc ctaacacgtg ttgttcaggg ttttctaaag agattcctat tttcttggat 2220 gcacaaatta cctattgcca cacggccaac aacatgacaa cgtcctatac agactatcct 2280 gaagtgaaag gttcttgggg taatgatacc ctgggcttaa ctttgtctac tagcgtacct 2340 atcccggtat ttagttcttc tatctttgat agttatgcac cgtttgcaaa attacaagtt 2400 gtctatgcgc accaagatga ctttaaagaa ccaacaacag aaggccgggt ctttgaaagc 2460 agcgatcttc tcaacgtttc tgtacctata ggtataaaat ttgagaaact ctcctatgga 2520 gagagaagtg cttatgatct tacactgatg tatatacctg atgtgtaccg tcataatcca 2580 agctgtatga caggattggc gatcaatgac gtttcctggt taaccacagc tacgaatctt 2640 gctagacaag ctttcatagt tcgcgcgggt aaccatattg ccttaacctc tggtgttgag 2700 atgttcagtc agtttggttt cgaattacga agctcttcaa gaaattataa cgtagatctt 2760 ggcgctaagg tcgcgttcta a 2781 57 926 PRT Chlamydia psittaci 57 Met Arg Pro Ser Leu Tyr Lys Ile Leu Ile Ser Ser Thr Leu Thr Leu 1 5 10 15 Pro Ile Ser Phe His Phe Ser Gln Leu His Ala Glu Val Ala Leu Thr 20 25 30 Gln Glu Ser Ile Leu Asp Ala Asn Gly Ala Phe Ser Pro Gln Ser Thr 35 40 45 Ser Thr Ala Gly Gly Thr Ile Tyr Asn Val Glu Ser Asp Ile Ser Ile 50 55 60 Val Asp Val Gly Gln Thr Ala Ala Leu Ala Ser Ser Ala Phe Val Gln 65 70 75 80 Thr Ala Asp Asn Leu Thr Phe Lys Gly Asn Asn His Ser Leu Ser Ile 85 90 95 Thr Asn Ala Asn Ala Gly Ala Asn Pro Ala Gly Ile Asn Val Asn Thr 100 105 110 Ala Asp Lys Ile Leu Thr Leu Thr Asp Phe Ser Lys Leu Ser Phe Lys 115 120 125 Glu Cys Pro Ser Ser Leu Val Asn Thr Gly Lys Gly Ala Met Lys Ser 130 135 140 Gly Gly Ala Leu Asn Leu Ala Asn Asn Ala Ser Ile Leu Phe Asp Gln 145 150 155 160 Asn Tyr Ser Ala Glu Asn Gly Gly Ala Ile Ser Cys Lys Ala Phe Ser 165 170 175 Leu Thr Gly Ser Ser Lys Glu Ile Ser Phe Thr Thr Asn Ser Thr Ala 180 185 190 Lys Lys Gly Gly Ala Ile Ala Ala Thr Gly Ile Ala His Leu Ser Asp 195 200 205 Asn Gln Gly Thr Ile Arg Phe Ser Gly Asn Thr Ala Val Asn Ser Gly 210 215 220 Gly Ala Val Tyr Ser Glu Ala Ser Met Thr Ile Ala Gly Asn Asn His 225 230 235 240 Val Ala Phe Ser Asn Asn Ala Val Ser Gly Ser Ser Asp Gly Cys Gly 245 250 255 Gly Ala Ile His Cys Ser Lys Thr Gly Ser Ala Pro Thr Leu Thr Ile 260 265 270 Arg Asp Asn Lys Val Leu Ile Phe Glu Glu Asn Thr Ser Ser Ala Lys 275 280 285 Gly Gly Ala Ile Tyr Thr Asp Lys Leu Ile Leu Thr Ser Gly Gly Pro 290 295 300 Thr Ala Phe Ile Asn Asn Lys Val Thr His Ala Thr Pro Lys Gly Gly 305 310 315 320 Ala Ile Gly Ile Ala Ala Asn Gly Glu Cys Ser Leu Thr Ala Glu His 325 330 335 Gly Asp Ile Thr Phe Asp Asn Asn Leu Met Ala Thr Gln Asp Asn Ala 340 345 350 Thr Ile Lys Arg Asn Ala Ile Asn Ile Glu Gly Asn Gly Lys Phe Val 355 360 365 Asn Leu Arg Ala Ala Ser Gly Lys Thr Ile Ser Phe Tyr Asp Pro Ile 370 375 380 Thr Val Glu Gly Asn Ala Ala Asp Leu Leu Thr Leu Asn Lys Ala Glu 385 390 395 400 Gly Asp Lys Thr Tyr Asn Gly Arg Ile Ile Phe Ser Gly Glu Lys Leu 405 410 415 Thr Glu Glu Gln Ala Ala Val Ala Asp Asn Leu Lys Thr Thr Phe Thr 420 425 430 Gln Pro Ile Thr Leu Ala Ala Gly Glu Leu Val Leu Arg Ser Gly Val 435 440 445 Glu Val Glu Ala Lys Thr Val Val Gln Thr Ala Gly Ser Leu Ile Leu 450 455 460 Met Asp Ala Gly Thr Lys Leu Ser Ala Lys Thr Glu Asp Ala Thr Leu 465 470 475 480 Thr Asn Leu Ala Ile Asn Pro Asn Thr Leu Asp Gly Lys Lys Phe Ala 485 490 495 Val Val Asp Ala Val Ala Ala Gly Lys Asn Val Thr Leu Ser Gly Ala 500 505 510 Ile Gly Val Ile Asp Pro Thr Gly Lys Phe Tyr Glu Asn His Lys Leu 515 520 525 Asn Asp Thr Leu Ala Leu Gly Gly Ile Gln Leu Ser Gly Lys Gly Ser 530 535 540 Val Thr Thr Thr Asn Val Pro Ser His Val Val Gly Val Ala Glu Thr 545 550 555 560 His Tyr Gly Tyr Gln Gly Asn Trp Ser Val Ser Trp Val Lys Asp Asn 565 570 575 Asn Ser Asp Pro Lys Thr Gln Thr Ala Ile Phe Thr Trp Asn Lys Thr 580 585 590 Gly Tyr Val Pro Asn Pro Glu Arg Arg Ala Pro Leu Val Leu Asn Ser 595 600 605 Leu Trp Gly Ser Phe Ile Asp Leu Arg Ser Ile Gln Asp Val Leu Glu 610 615 620 Arg Ser Val Asp Ser Ile Leu Glu Thr Arg Arg Gly Leu Trp Val Ser 625 630 635 640 Gly Ile Gly Asn Phe Phe His Lys Asp Arg Asn Ala Glu Asn Arg Lys 645 650 655 Phe Arg His Ile Ser Ser Gly Tyr Val Leu Gly Ala Thr Thr Asn Thr 660 665 670 Ser Arg Glu Asp Ser Leu Ser Val Ala Phe Cys Gln Leu Phe Ala Lys 675 680 685 Asp Lys Asp Tyr Leu Val Ser Lys Asn Ala Ala Asn Val Tyr Ala Gly 690 695 700 Ser Val Tyr Tyr Gln His Val Ser Lys Phe Asp Asp Leu Thr Arg Leu 705 710 715 720 Phe Asn Gly Pro Asn Thr Cys Cys Ser Gly Phe Ser Lys Glu Ile Pro 725 730 735 Ile Phe Leu Asp Ala Gln Ile Thr Tyr Cys His Thr Ala Asn Asn Met 740 745 750 Thr Thr Ser Tyr Thr Asp Tyr Pro Glu Val Lys Gly Ser Trp Gly Asn 755 760 765 Asp Thr Leu Gly Leu Thr Leu Ser Thr Ser Val Pro Ile Pro Val Phe 770 775 780 Ser Ser Ser Ile Phe Asp Ser Tyr Ala Pro Phe Ala Lys Leu Gln Val 785 790 795 800 Val Tyr Ala His Gln Asp Asp Phe Lys Glu Pro Thr Thr Glu Gly Arg 805 810 815 Val Phe Glu Ser Ser Asp Leu Leu Asn Val Ser Val Pro Ile Gly Ile 820 825 830 Lys Phe Glu Lys Leu Ser Tyr Gly Glu Arg Ser Ala Tyr Asp Leu Thr 835 840 845 Leu Met Tyr Ile Pro Asp Val Tyr Arg His Asn Pro Ser Cys Met Thr 850 855 860 Gly Leu Ala Ile Asn Asp Val Ser Trp Leu Thr Thr Ala Thr Asn Leu 865 870 875 880 Ala Arg Gln Ala Phe Ile Val Arg Ala Gly Asn His Ile Ala Leu Thr 885 890 895 Ser Gly Val Glu Met Phe Ser Gln Phe Gly Phe Glu Leu Arg Ser Ser 900 905 910 Ser Arg Asn Tyr Asn Val Asp Leu Gly Ala Lys Val Ala Phe 915 920 925 58 559 DNA Chlamydia psittaci 58 tgtgttcatt ctttagcagg agttgcattt acgttgtttc tctgtgagca tatgtttacc 60 aatatgcttg cttcttctta ttttaaggaa ggcagtggtt ttgttcagtt agtgagcaaa 120 tttcatcaga ttcctggtct gaagatcata gaaattgttt ttttagccct accgtttact 180 tgtcacgcta tcctaggtat tttctatctt tttcaagcgc aaactaattc acgggcttct 240 gacggcagaa aacccgcgtt aatctatgcg agaaatcttg cctatacttg gcagagaaga 300 actgcttgga ttttactttt cggtcttatt tttcacgtag ttcagtttcg ttttcttcgt 360 tatcctattc atgtagagct gcatgggcaa acatactatg ttgtcgatat tgacgcttct 420 cggtatgcgg cgatagtgcg gggtacacaa ggatttttta ctataaattt ttcagctcct 480 caacttgaaa cgattcgttt ggataaagag gatcttgacg gcagcgcagt ttctcaatta 540 ttagacagaa aagcgtatc 559 59 186 PRT Chlamydia psittaci 59 Cys Val His Ser Leu Ala Gly Val Ala Phe Thr Leu Phe Leu Cys Glu 1 5 10 15 His Met Phe Thr Asn Met Leu Ala Ser Ser Tyr Phe Lys Glu Gly Ser 20 25 30 Gly Phe Val Gln Leu Val Ser Lys Phe His Gln Ile Pro Gly Leu Lys 35 40 45 Ile Ile Glu Ile Val Phe Leu Ala Leu Pro Phe Thr Cys His Ala Ile 50 55 60 Leu Gly Ile Phe Tyr Leu Phe Gln Ala Gln Thr Asn Ser Arg Ala Ser 65 70 75 80 Asp Gly Arg Lys Pro Ala Leu Ile Tyr Ala Arg Asn Leu Ala Tyr Thr 85 90 95 Trp Gln Arg Arg Thr Ala Trp Ile Leu Leu Phe Gly Leu Ile Phe His 100 105 110 Val Val Gln Phe Arg Phe Leu Arg Tyr Pro Ile His Val Glu Leu His 115 120 125 Gly Gln Thr Tyr Tyr Val Val Asp Ile Asp Ala Ser Arg Tyr Ala Ala 130 135 140 Ile Val Arg Gly Thr Gln Gly Phe Phe Thr Ile Asn Phe Ser Ala Pro 145 150 155 160 Gln Leu Glu Thr Ile Arg Leu Asp Lys Glu Asp Leu Asp Gly Ser Ala 165 170 175 Val Ser Gln Leu Leu Asp Arg Lys Ala Tyr 180 185 60 687 DNA Chlamydia psittaci 60 atgatgaatg aaaaggaatc atgttctgag gctactcaga ggtcatggaa gtactacact 60 agctttgttt tacgttgtgt tcattcttta gcaggagttg catttacgtt gtttctctgt 120 gagcatatgt ttaccaatat gcttgcttct tcttatttta aggaaggcag tggttttgtt 180 cagttagtga gcaaatttca tcagattcct ggtctgaaga tcatagaaat tgttttttta 240 gccctaccgt ttacttgtca cgctatccta ggtattttct atctttttca agcgcaaact 300 aattcacggg cttctgacgg cagaaaaccc gcgttaatct atgcgagaaa tcttgcctat 360 acttggcaga gaagaactgc ttggatttta cttttcggtc ttatttttca cgtagttcag 420 tttcgttttc ttcgttatcc tattcatgta gagctgcatg ggcaaacata ctatgttgtc 480 gatattgacg cttctcggta tgcggcgata gtgcggggta cacaaggatt ttttactata 540 aatttttcag ctcctcaact tgaaacgatt cgtttggata aagaggatct tgacggcagc 600 gcagtttctc aattattaga cagaaaagcg tatctcctga ctcctaatgt tggaccgctt 660 ttctttatgt tgttcgggat tctttag 687 61 228 PRT Chlamydia psittaci 61 Met Met Asn Glu Lys Glu Ser Cys Ser Glu Ala Thr Gln Arg Ser Trp 1 5 10 15 Lys Tyr Tyr Thr Ser Phe Val Leu Arg Cys Val His Ser Leu Ala Gly 20 25 30 Val Ala Phe Thr Leu Phe Leu Cys Glu His Met Phe Thr Asn Met Leu 35 40 45 Ala Ser Ser Tyr Phe Lys Glu Gly Ser Gly Phe Val Gln Leu Val Ser 50 55 60 Lys Phe His Gln Ile Pro Gly Leu Lys Ile Ile Glu Ile Val Phe Leu 65 70 75 80 Ala Leu Pro Phe Thr Cys His Ala Ile Leu Gly Ile Phe Tyr Leu Phe 85 90 95 Gln Ala Gln Thr Asn Ser Arg Ala Ser Asp Gly Arg Lys Pro Ala Leu 100 105 110 Ile Tyr Ala Arg Asn Leu Ala Tyr Thr Trp Gln Arg Arg Thr Ala Trp 115 120 125 Ile Leu Leu Phe Gly Leu Ile Phe His Val Val Gln Phe Arg Phe Leu 130 135 140 Arg Tyr Pro Ile His Val Glu Leu His Gly Gln Thr Tyr Tyr Val Val 145 150 155 160 Asp Ile Asp Ala Ser Arg Tyr Ala Ala Ile Val Arg Gly Thr Gln Gly 165 170 175 Phe Phe Thr Ile Asn Phe Ser Ala Pro Gln Leu Glu Thr Ile Arg Leu 180 185 190 Asp Lys Glu Asp Leu Asp Gly Ser Ala Val Ser Gln Leu Leu Asp Arg 195 200 205 Lys Ala Tyr Leu Leu Thr Pro Asn Val Gly Pro Leu Phe Phe Met Leu 210 215 220 Phe Gly Ile Leu 225 62 1329 DNA Chlamydia psittaci 62 atgactctac aaccctacca agcatcctct agaaagtacc gtccacaaat ctttcgagaa 60 attctaggtc agagctctgt tgtcgctgta ttaaaaaatg ccttggtctt caaccgagcc 120 gcccacgcct atctattttc tggaattcgt ggtacaggga aaaccacact agctcgcatt 180 ttagcaaaag ctctgaactg cgtgcatctt agcgaggatg gcgagccctg caaccagtgt 240 ttttcttgta aagagattgc ttcaggatcc tctttagacg ttttagaaat tgacggagcc 300 tcccaccgtg gtatcgaaga tatccgtcaa attaatgaaa ctgtattatt cactcctgta 360 aaagcaaagt ttaaaattta tatcatagat gaagttcata tgctcactaa ggaagccttc 420 aatgctttat tgaagacttt agaagagcct ccacaacatg taaaattttt ctttgcaact 480 acagaaatcc ataaaattcc cggaactatt ttaagtcgtt gtcaaaaaat gcatcttcaa 540 aggattcctg aaaaaacgat cctggagaag ctatcgctta tggctcaaga tgaccatatt 600 gaggcgtcgc aagaagcatt ggcgccgatc gcccgtgcag cacaaggaag cttgcgtgat 660 gcagaatctc tttatgacta cgtaatatct ttatttccta aatctctctc tcccgacacg 720 gttgcccaag ctttaggctt tgcttcccaa gattctctcc ggactttaga caatgcgatt 780 cttcaaaggg actatgcgac agccttaggg atcgtaacgg acttcttaaa ttctggggta 840 gcacctgtca catttctcca tgaccttaca ttattttatc gtaatcttct tcttacgaat 900 tctacaacaa gcaagttcag ctctcagtat aagacggagc agcttctaga aatcatagat 960 ttccttggag aatctgctaa gcacctacaa aataccatct tcgaacagac atttttagaa 1020 accgtcatca ttcatatcat tcgcatttat caaaggcctg ttttatcaga gttgatctct 1080 tctattaaga gtcggcagtt tgaagggctt cgcaatatta aggagcccac cttgacgcag 1140 caagtatcag ctcctcaacc tcagcccacc tacaaagaac agagtttttt agagaaaaaa 1200 aatcaacctg ctgcggaagg taaaattata tctgtagaag ttaaaagctc agcttcaata 1260 aaatctgcag ctgtagacac attattacag tttgctgttg tagaattttc aggaatttta 1320 agacaataa 1329 63 442 PRT Chlamydia psittaci 63 Met Thr Leu Gln Pro Tyr Gln Ala Ser Ser Arg Lys Tyr Arg Pro Gln 1 5 10 15 Ile Phe Arg Glu Ile Leu Gly Gln Ser Ser Val Val Ala Val Leu Lys 20 25 30 Asn Ala Leu Val Phe Asn Arg Ala Ala His Ala Tyr Leu Phe Ser Gly 35 40 45 Ile Arg Gly Thr Gly Lys Thr Thr Leu Ala Arg Ile Leu Ala Lys Ala 50 55 60 Leu Asn Cys Val His Leu Ser Glu Asp Gly Glu Pro Cys Asn Gln Cys 65 70 75 80 Phe Ser Cys Lys Glu Ile Ala Ser Gly Ser Ser Leu Asp Val Leu Glu 85 90 95 Ile Asp Gly Ala Ser His Arg Gly Ile Glu Asp Ile Arg Gln Ile Asn 100 105 110 Glu Thr Val Leu Phe Thr Pro Val Lys Ala Lys Phe Lys Ile Tyr Ile 115 120 125 Ile Asp Glu Val His Met Leu Thr Lys Glu Ala Phe Asn Ala Leu Leu 130 135 140 Lys Thr Leu Glu Glu Pro Pro Gln His Val Lys Phe Phe Phe Ala Thr 145 150 155 160 Thr Glu Ile His Lys Ile Pro Gly Thr Ile Leu Ser Arg Cys Gln Lys 165 170 175 Met His Leu Gln Arg Ile Pro Glu Lys Thr Ile Leu Glu Lys Leu Ser 180 185 190 Leu Met Ala Gln Asp Asp His Ile Glu Ala Ser Gln Glu Ala Leu Ala 195 200 205 Pro Ile Ala Arg Ala Ala Gln Gly Ser Leu Arg Asp Ala Glu Ser Leu 210 215 220 Tyr Asp Tyr Val Ile Ser Leu Phe Pro Lys Ser Leu Ser Pro Asp Thr 225 230 235 240 Val Ala Gln Ala Leu Gly Phe Ala Ser Gln Asp Ser Leu Arg Thr Leu 245 250 255 Asp Asn Ala Ile Leu Gln Arg Asp Tyr Ala Thr Ala Leu Gly Ile Val 260 265 270 Thr Asp Phe Leu Asn Ser Gly Val Ala Pro Val Thr Phe Leu His Asp 275 280 285 Leu Thr Leu Phe Tyr Arg Asn Leu Leu Leu Thr Asn Ser Thr Thr Ser 290 295 300 Lys Phe Ser Ser Gln Tyr Lys Thr Glu Gln Leu Leu Glu Ile Ile Asp 305 310 315 320 Phe Leu Gly Glu Ser Ala Lys His Leu Gln Asn Thr Ile Phe Glu Gln 325 330 335 Thr Phe Leu Glu Thr Val Ile Ile His Ile Ile Arg Ile Tyr Gln Arg 340 345 350 Pro Val Leu Ser Glu Leu Ile Ser Ser Ile Lys Ser Arg Gln Phe Glu 355 360 365 Gly Leu Arg Asn Ile Lys Glu Pro Thr Leu Thr Gln Gln Val Ser Ala 370 375 380 Pro Gln Pro Gln Pro Thr Tyr Lys Glu Gln Ser Phe Leu Glu Lys Lys 385 390 395 400 Asn Gln Pro Ala Ala Glu Gly Lys Ile Ile Ser Val Glu Val Lys Ser 405 410 415 Ser Ala Ser Ile Lys Ser Ala Ala Val Asp Thr Leu Leu Gln Phe Ala 420 425 430 Val Val Glu Phe Ser Gly Ile Leu Arg Gln 435 440 64 1479 DNA Chlamydia psittaci 64 atgtatcgat atagtgcttt agaattagca aaagctgtga ctttagggga actgacagcc 60 acaggggtga ctcaacattt ttttcataga atagaagaag ctgaggggca ggtaggtgcc 120 tttatttcct tgtgtaagga acaagcttta gaacaggcag agctcataga taaaaagcgt 180 tcgcgtggag aacctttagg aaaactcgca ggtgttcctg taggaattaa agataatatt 240 cacgttacag gcctgaagac aacatgcgcc tctcgtgtgc tcgagaatta tcaaccaccg 300 tttgatgcta ctgttgtaga aagaatcaaa aaagaagatg ggattatctt aggcaaactc 360 aatatggatg agtttgctat gggatcaaca acgctatatt ctgcttttca tcctacccac 420 aacccctggg atttatctcg tgttcctgga ggttcttcag ggggatctgc ggccgcagtt 480 tctgctagat tttgtcccgt agccctagga tcagataccg gaggatccat ccgtcagccc 540 gcagcatttt gtggtgttgt aggttttaag ccttcctacg gagccgtttc gcgttacggg 600 cttgtagcct ttgcctcttc gctagatcaa atcggtcctt tagccaatac tgtagaagac 660 gtcgccctaa tgatggatgt gttttctggt agagatccta aagatgcaac ctcaagagag 720 tttttccgtg attcttttat gagcaagttg tctacggagg ttcctaaagt gattggggtg 780 cctagaacat ttttagaggg actccgtgat gatattaggg agaatttctt ctcttcatta 840 gccatttttg aaggagaagg aacccatctt gtggatgtgg agttggatat tctcagccac 900 gctgtatcta tatattacat tttagcatct gctgaagctg ccacgaattt agcaaggttc 960 gatggggtgc gttatggata tcgttctcct caagcgcata ccatcagcca actctacgat 1020 ctctcacgtg gagaaggatt tggcaaagag gtcatgcgca gaatcctctt agggaactat 1080 gtcttgtctg cggagagaca gaatgtttat tataagaaag ctacggcagt gcgtgctaag 1140 attgtaaaag catttagaac tgcatttgaa aagtgtgaaa tcttagccat gcccgtctgt 1200 tctagccccg cgtttgaaat aggagaaatt ctagatcctg tgactttata tctacaggat 1260 atctatactg tagctatgaa tttagcgtat cttcctgcca ttgccgtacc ctctggattt 1320 tctaaggagg gcctgccctt aggcctacag attatcggac agcaaggaca agaccaacaa 1380 gtgtgccaag tgggttacag tttccaagag catgcgcaaa ttaagcaatt gttttctaag 1440 agatatgcca aaagtgttgt tctaggaggt caatcatga 1479 65 492 PRT Chlamydia psittaci 65 Met Tyr Arg Tyr Ser Ala Leu Glu Leu Ala Lys Ala Val Thr Leu Gly 1 5 10 15 Glu Leu Thr Ala Thr Gly Val Thr Gln His Phe Phe His Arg Ile Glu 20 25 30 Glu Ala Glu Gly Gln Val Gly Ala Phe Ile Ser Leu Cys Lys Glu Gln 35 40 45 Ala Leu Glu Gln Ala Glu Leu Ile Asp Lys Lys Arg Ser Arg Gly Glu 50 55 60 Pro Leu Gly Lys Leu Ala Gly Val Pro Val Gly Ile Lys Asp Asn Ile 65 70 75 80 His Val Thr Gly Leu Lys Thr Thr Cys Ala Ser Arg Val Leu Glu Asn 85 90 95 Tyr Gln Pro Pro Phe Asp Ala Thr Val Val Glu Arg Ile Lys Lys Glu 100 105 110 Asp Gly Ile Ile Leu Gly Lys Leu Asn Met Asp Glu Phe Ala Met Gly 115 120 125 Ser Thr Thr Leu Tyr Ser Ala Phe His Pro Thr His Asn Pro Trp Asp 130 135 140 Leu Ser Arg Val Pro Gly Gly Ser Ser Gly Gly Ser Ala Ala Ala Val 145 150 155 160 Ser Ala Arg Phe Cys Pro Val Ala Leu Gly Ser Asp Thr Gly Gly Ser 165 170 175 Ile Arg Gln Pro Ala Ala Phe Cys Gly Val Val Gly Phe Lys Pro Ser 180 185 190 Tyr Gly Ala Val Ser Arg Tyr Gly Leu Val Ala Phe Ala Ser Ser Leu 195 200 205 Asp Gln Ile Gly Pro Leu Ala Asn Thr Val Glu Asp Val Ala Leu Met 210 215 220 Met Asp Val Phe Ser Gly Arg Asp Pro Lys Asp Ala Thr Ser Arg Glu 225 230 235 240 Phe Phe Arg Asp Ser Phe Met Ser Lys Leu Ser Thr Glu Val Pro Lys 245 250 255 Val Ile Gly Val Pro Arg Thr Phe Leu Glu Gly Leu Arg Asp Asp Ile 260 265 270 Arg Glu Asn Phe Phe Ser Ser Leu Ala Ile Phe Glu Gly Glu Gly Thr 275 280 285 His Leu Val Asp Val Glu Leu Asp Ile Leu Ser His Ala Val Ser Ile 290 295 300 Tyr Tyr Ile Leu Ala Ser Ala Glu Ala Ala Thr Asn Leu Ala Arg Phe 305 310 315 320 Asp Gly Val Arg Tyr Gly Tyr Arg Ser Pro Gln Ala His Thr Ile Ser 325 330 335 Gln Leu Tyr Asp Leu Ser Arg Gly Glu Gly Phe Gly Lys Glu Val Met 340 345 350 Arg Arg Ile Leu Leu Gly Asn Tyr Val Leu Ser Ala Glu Arg Gln Asn 355 360 365 Val Tyr Tyr Lys Lys Ala Thr Ala Val Arg Ala Lys Ile Val Lys Ala 370 375 380 Phe Arg Thr Ala Phe Glu Lys Cys Glu Ile Leu Ala Met Pro Val Cys 385 390 395 400 Ser Ser Pro Ala Phe Glu Ile Gly Glu Ile Leu Asp Pro Val Thr Leu 405 410 415 Tyr Leu Gln Asp Ile Tyr Thr Val Ala Met Asn Leu Ala Tyr Leu Pro 420 425 430 Ala Ile Ala Val Pro Ser Gly Phe Ser Lys Glu Gly Leu Pro Leu Gly 435 440 445 Leu Gln Ile Ile Gly Gln Gln Gly Gln Asp Gln Gln Val Cys Gln Val 450 455 460 Gly Tyr Ser Phe Gln Glu His Ala Gln Ile Lys Gln Leu Phe Ser Lys 465 470 475 480 Arg Tyr Ala Lys Ser Val Val Leu Gly Gly Gln Ser 485 490 66 1962 DNA Chlamydia psittaci 66 atgagctacc gtaaacgttc gactctaatt gttctaggag tgtttgctct ttatgctctt 60 ctagtattgc gttattataa aattcaaatt tgtgaaggag accactgggc cgcagaagct 120 ctcgggcaac acgaattttg tgtccgtgat ccttttcgaa ggggcacctt ttttgctaac 180 acgacagtac gtaagggaga caaagacctt cagcagcctt tcgctgtcga tattacaaaa 240 tttcaccttt gtgcagatcc tttagctatt cccgaatgtc atcgtgatga gatcatccaa 300 gggattctcc aatttattga ggggcagacc tacgacgacc tctccctaaa gttagataag 360 aaatctcggt attgtaagct gtatccttta ttagatgttt ctgtccatga ccggctatcc 420 ctttggtgga aaggatatgc aacaaagcat cgcttaccaa caaacgccct attttttatt 480 acggactacc aacgctcgta tccttttggg aagctccttg gacaagttct ccatacctta 540 agagaaatta aggatgagaa aacaggaaaa gcctttccca caggcgggat ggaggcgtac 600 tttaatcata ttctggaagg ggacgttgga gagagaaagc tgttgcgttc tcctttgaac 660 cgtttagata cgaatcgtgt tatcaaactg cctaaagatg gctctgatat ctaccttacg 720 atcaatcctg tgatccagac cattgcagag gaagaactcg aacggggcgt gctagaagct 780 aaagcccagg ggggtaggct cattctaatg aactcccaaa caggagagat tcttgcactg 840 gctcaatatc cgtttttcga tcccacaaat tataaggaat acttcaataa caaagagcgc 900 atcgaacata cgaaggtatc ttttgtgagc gatgtttttg aacccgggtc gatcatgaaa 960 cctttgactg tggcgattgc tttacaagct aacgaagagg ctagcttaaa atcgcagaaa 1020 aagatttttg atcctgaaga acctatcgat gtgaccagga cactcttccc tggacgaaaa 1080 ggatctccgc ttaaggatat ttctagaaac tctcaattga atatgtacat ggctatccag 1140 aaatcttcga atgtctatgt agctcagctg gctgaccgca tcatacaatc tttaggagtg 1200 gcctggtacc aacagaagtt gctagctctg ggatttggaa gaaaaacagg gatcgagctt 1260 cccagtgagg cctctggttt ggtgccttct ccccatcgtt tccatattaa tggttccctg 1320 gaatggtcct tatctactcc atattctttg gctatgggat ataatatttt ggcaacaggg 1380 atacaaatgg ttcaagccta cgctatcctt gcaaacggag gttatgccgt ccggcccact 1440 ttagtaaaaa agatcgtctc tgcttcagga gaggaatatc atcttcctac taaagagaag 1500 acacgactct tttcagaaga aattactaga gaagttgttc gtgccatgcg ttttacaacg 1560 ttacccggag gttcgggatt tcgagcctct cctaagcatc actctagtgc tgggaaaaca 1620 ggaactacag aaaagatgat tcatggaaaa tatgataaac gccgtcatat tgcttctttt 1680 ataggtttta ctcccgtaga gagctcggag ggaaatttcc cacctttagt gatgctcgtc 1740 tccatagatg atcctgaata tggtttgcga gccgacggca cgaaaaatta tatggggggg 1800 cgttgtgcgg cacccatttt ttctagggtt gctgaccgca cactcctcta tttagggatt 1860 cttccagaca agaagctaag aaattgcgac gaagaagctg ctgcattaaa gcgtctctat 1920 gaagaatgga atcgttctcc gaaacaaggg ggaacgaggt ga 1962 67 653 PRT Chlamydia psittaci 67 Met Ser Tyr Arg Lys Arg Ser Thr Leu Ile Val Leu Gly Val Phe Ala 1 5 10 15 Leu Tyr Ala Leu Leu Val Leu Arg Tyr Tyr Lys Ile Gln Ile Cys Glu 20 25 30 Gly Asp His Trp Ala Ala Glu Ala Leu Gly Gln His Glu Phe Cys Val 35 40 45 Arg Asp Pro Phe Arg Arg Gly Thr Phe Phe Ala Asn Thr Thr Val Arg 50 55 60 Lys Gly Asp Lys Asp Leu Gln Gln Pro Phe Ala Val Asp Ile Thr Lys 65 70 75 80 Phe His Leu Cys Ala Asp Pro Leu Ala Ile Pro Glu Cys His Arg Asp 85 90 95 Glu Ile Ile Gln Gly Ile Leu Gln Phe Ile Glu Gly Gln Thr Tyr Asp 100 105 110 Asp Leu Ser Leu Lys Leu Asp Lys Lys Ser Arg Tyr Cys Lys Leu Tyr 115 120 125 Pro Leu Leu Asp Val Ser Val His Asp Arg Leu Ser Leu Trp Trp Lys 130 135 140 Gly Tyr Ala Thr Lys His Arg Leu Pro Thr Asn Ala Leu Phe Phe Ile 145 150 155 160 Thr Asp Tyr Gln Arg Ser Tyr Pro Phe Gly Lys Leu Leu Gly Gln Val 165 170 175 Leu His Thr Leu Arg Glu Ile Lys Asp Glu Lys Thr Gly Lys Ala Phe 180 185 190 Pro Thr Gly Gly Met Glu Ala Tyr Phe Asn His Ile Leu Glu Gly Asp 195 200 205 Val Gly Glu Arg Lys Leu Leu Arg Ser Pro Leu Asn Arg Leu Asp Thr 210 215 220 Asn Arg Val Ile Lys Leu Pro Lys Asp Gly Ser Asp Ile Tyr Leu Thr 225 230 235 240 Ile Asn Pro Val Ile Gln Thr Ile Ala Glu Glu Glu Leu Glu Arg Gly 245 250 255 Val Leu Glu Ala Lys Ala Gln Gly Gly Arg Leu Ile Leu Met Asn Ser 260 265 270 Gln Thr Gly Glu Ile Leu Ala Leu Ala Gln Tyr Pro Phe Phe Asp Pro 275 280 285 Thr Asn Tyr Lys Glu Tyr Phe Asn Asn Lys Glu Arg Ile Glu His Thr 290 295 300 Lys Val Ser Phe Val Ser Asp Val Phe Glu Pro Gly Ser Ile Met Lys 305 310 315 320 Pro Leu Thr Val Ala Ile Ala Leu Gln Ala Asn Glu Glu Ala Ser Leu 325 330 335 Lys Ser Gln Lys Lys Ile Phe Asp Pro Glu Glu Pro Ile Asp Val Thr 340 345 350 Arg Thr Leu Phe Pro Gly Arg Lys Gly Ser Pro Leu Lys Asp Ile Ser 355 360 365 Arg Asn Ser Gln Leu Asn Met Tyr Met Ala Ile Gln Lys Ser Ser Asn 370 375 380 Val Tyr Val Ala Gln Leu Ala Asp Arg Ile Ile Gln Ser Leu Gly Val 385 390 395 400 Ala Trp Tyr Gln Gln Lys Leu Leu Ala Leu Gly Phe Gly Arg Lys Thr 405 410 415 Gly Ile Glu Leu Pro Ser Glu Ala Ser Gly Leu Val Pro Ser Pro His 420 425 430 Arg Phe His Ile Asn Gly Ser Leu Glu Trp Ser Leu Ser Thr Pro Tyr 435 440 445 Ser Leu Ala Met Gly Tyr Asn Ile Leu Ala Thr Gly Ile Gln Met Val 450 455 460 Gln Ala Tyr Ala Ile Leu Ala Asn Gly Gly Tyr Ala Val Arg Pro Thr 465 470 475 480 Leu Val Lys Lys Ile Val Ser Ala Ser Gly Glu Glu Tyr His Leu Pro 485 490 495 Thr Lys Glu Lys Thr Arg Leu Phe Ser Glu Glu Ile Thr Arg Glu Val 500 505 510 Val Arg Ala Met Arg Phe Thr Thr Leu Pro Gly Gly Ser Gly Phe Arg 515 520 525 Ala Ser Pro Lys His His Ser Ser Ala Gly Lys Thr Gly Thr Thr Glu 530 535 540 Lys Met Ile His Gly Lys Tyr Asp Lys Arg Arg His Ile Ala Ser Phe 545 550 555 560 Ile Gly Phe Thr Pro Val Glu Ser Ser Glu Gly Asn Phe Pro Pro Leu 565 570 575 Val Met Leu Val Ser Ile Asp Asp Pro Glu Tyr Gly Leu Arg Ala Asp 580 585 590 Gly Thr Lys Asn Tyr Met Gly Gly Arg Cys Ala Ala Pro Ile Phe Ser 595 600 605 Arg Val Ala Asp Arg Thr Leu Leu Tyr Leu Gly Ile Leu Pro Asp Lys 610 615 620 Lys Leu Arg Asn Cys Asp Glu Glu Ala Ala Ala Leu Lys Arg Leu Tyr 625 630 635 640 Glu Glu Trp Asn Arg Ser Pro Lys Gln Gly Gly Thr Arg 645 650 68 819 DNA Chlamydia psittaci 68 atgaaaaaaa aattatcatt acttgtaggt ttaatttttg ttttgagttc ttgccataag 60 gaagatgctc agaataaaat acgtattgta gccagtccga cacctcatgc ggaattattg 120 gagagtttac aggaagaggc taaagatctt ggaatcaagc tgaaaatact tccagtagat 180 gattatcgta ttcctaatcg tttgcttttg gataaacaag tagatgcaaa ttactttcaa 240 catcaagctt ttcttgatga cgaatgcgag cgttatgatt gtaagggtga attagttgtt 300 atcgctaaag ttcatttgga acctcaagca atttattcta agaaacattc ttctttagag 360 cgcttaaaaa gccagaagaa actgactata gcgattcctg tggatcgtac gaatgctcag 420 cgtgctctac acttgttaga agagtgcgga ctcattgttt gcaaagggcc tgctaattta 480 aatatgacag ctaaagatgt ctgtgggaaa gaaaatagaa gtatcaacat attagaggtg 540 tcagctcctc ttcttgtcgg atctcttcct gacgttgatg ctgctgtcat tcctggaaat 600 tttgctatag cagcaaacct ttctccaaag aaagatagtc tttgtttaga ggatctttcg 660 gtatctaagt atacaaacct tgttgtcatt cgttctgaag acgtaggttc tcctaaaatg 720 ataaaattac agaagctgtt tcaatctcct tctgtacaac atttttttga tacaaaatat 780 catgggaata ttttgacaat gactcaagac aatggttag 819 69 272 PRT Chlamydia psittaci 69 Met Lys Lys Lys Leu Ser Leu Leu Val Gly Leu Ile Phe Val Leu Ser 1 5 10 15 Ser Cys His Lys Glu Asp Ala Gln Asn Lys Ile Arg Ile Val Ala Ser 20 25 30 Pro Thr Pro His Ala Glu Leu Leu Glu Ser Leu Gln Glu Glu Ala Lys 35 40 45 Asp Leu Gly Ile Lys Leu Lys Ile Leu Pro Val Asp Asp Tyr Arg Ile 50 55 60 Pro Asn Arg Leu Leu Leu Asp Lys Gln Val Asp Ala Asn Tyr Phe Gln 65 70 75 80 His Gln Ala Phe Leu Asp Asp Glu Cys Glu Arg Tyr Asp Cys Lys Gly 85 90 95 Glu Leu Val Val Ile Ala Lys Val His Leu Glu Pro Gln Ala Ile Tyr 100 105 110 Ser Lys Lys His Ser Ser Leu Glu Arg Leu Lys Ser Gln Lys Lys Leu 115 120 125 Thr Ile Ala Ile Pro Val Asp Arg Thr Asn Ala Gln Arg Ala Leu His 130 135 140 Leu Leu Glu Glu Cys Gly Leu Ile Val Cys Lys Gly Pro Ala Asn Leu 145 150 155 160 Asn Met Thr Ala Lys Asp Val Cys Gly Lys Glu Asn Arg Ser Ile Asn 165 170 175 Ile Leu Glu Val Ser Ala Pro Leu Leu Val Gly Ser Leu Pro Asp Val 180 185 190 Asp Ala Ala Val Ile Pro Gly Asn Phe Ala Ile Ala Ala Asn Leu Ser 195 200 205 Pro Lys Lys Asp Ser Leu Cys Leu Glu Asp Leu Ser Val Ser Lys Tyr 210 215 220 Thr Asn Leu Val Val Ile Arg Ser Glu Asp Val Gly Ser Pro Lys Met 225 230 235 240 Ile Lys Leu Gln Lys Leu Phe Gln Ser Pro Ser Val Gln His Phe Phe 245 250 255 Asp Thr Lys Tyr His Gly Asn Ile Leu Thr Met Thr Gln Asp Asn Gly 260 265 270 

What is claimed is:
 1. A vaccine comprising: (a) a pharmaceutically acceptable carrier, and (b) at least one polynucleotide having a Chlamydia sequence.
 2. The vaccine of claim 1, wherein the at least one polynucleotide has a Chlamydia psittaci sequence.
 3. The vaccine of claim 1, wherein the at least one polynucleotide has a Chlamydia pneumoniae sequence.
 4. The vaccine of claim 1, wherein the at least one polynucleotide has a sequence isolated from a Chlamydia genomic DNA expression library.
 5. The vaccine of claim 4, wherein the at least one polynucleotide has a sequence isolated from a Chlamydia psittaci genomic DNA expression library.
 6. The vaccine of claim 1, wherein the at least one polynucleotide has a sequence of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO: 58, or SEQ ID NO:60, or fragment thereof.
 7. The vaccine of claim 6, wherein the at least one polynucleotide has a sequence of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, or SEQ ID NO:26, or fragment thereof.
 8. The vaccine of claim 6, wherein the at least one polynucleotide has a sequence of SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:14, SEQ ID NO:20, or SEQ ID NO:24, or fragment thereof.
 9. The vaccine of claim 1, wherein the at least one polynucleotide has a sequence of SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, or SEQ ID NO:68, or fragment thereof.
 10. The vaccine of claim 1, comprising a polynucleotide encoding an antigen having a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, or SEQ ID NO:61, or an antigenic fragment thereof.
 11. The vaccine of claim 1, comprising a polynucleotide encoding a antigen having a sequence of SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, or SEQ ID NO:69, or an antigenic fragment thereof.
 12. The vaccine of claim 1, wherein the polynucleotide is comprised in a genetic immunization vector.
 13. The vaccine of claim 12, wherein the vector comprises a gene encoding a mouse ubiquitin fusion polypeptide.
 14. The vaccine of claim 12, wherein the vector comprises a promoter operable in eukaryotic cells.
 15. The vaccine of claim 14, wherein the promoter is a CMV promoter.
 16. The vaccine of claim 1, wherein the polynucleotide is cloned into a viral expression vector.
 17. The vaccine of claim 16, wherein the viral expression vector is selected from the group consisting of adenovirus, adeno-associated virus, retrovirus and herpes-simplex virus.
 18. The vaccine of claim 1, comprising at least a first polynucleotide having a Chlamydia psittaci sequence and a second polynucleotide having a sequence, wherein the first polynucleotide and the second polynucleotide have different sequences.
 19. The vaccine of claim 6, wherein the first polynucleotide has a sequence of SEQ ID NO:50.
 20. A vaccine comprising: (a) a pharmaceutically acceptable carrier; and (b) at least one Chlamydia antigen.
 21. The vaccine of claim 20, wherein the at least one Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, or SEQ ID NO:61, or an antigenic fragment thereof.
 22. The vaccine of claim 20, wherein the at least one Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, or SEQ ID NO:27, or an antigenic fragment thereof.
 23. The vaccine of claim 20, wherein the at least one Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:11, SEQ ID NO: 15, SEQ ID NO:21, or SEQ ID NO:25, or an antigenic fragment thereof.
 24. The vaccine of claim 20, wherein the at least one Chlamydia antigen has a sequence of SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, or SEQ ID NO:69, or an antigenic fragment thereof.
 25. A method of immunizing an animal comprising providing to the animal at least one Chlamydia antigen, or an antigenic fragment thereof, in an amount effective to induce an immune response.
 26. The method of claim 25, wherein the provision of the at least one Chlamydia antigen comprises: (a) preparing a cloned expression library from fragmented genomic DNA, cDNA or sequenced genes of Chlamydia; (b) administering at least one clone of the library in a pharmaceutically acceptable carrier into the animal; and (c) expressing at least one Chlamydia antigen in the animal.
 27. The method of claim 26, herein the expression library comprises at least one or more polynucleotide having a sequence of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:052:, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO: 58, or SEQ ID NO:60, or fragment thereof.
 28. The method of claim 26, herein the expression library comprises at least one or more polynucleotide having a sequence of SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, or SEQ ID NO:68, or fragment thereof.
 29. The method of claim 27, wherein the polynucleotide is administered by a intramuscular injection or epidermal injection.
 30. The method of claim 29, wherein the intramuscular injection is at least 1.0 μg to 200 μg of the polynucleotide.
 31. The method of claim 29, wherein a second intramuscular injection and epidermal injection are administered at least about three weeks after the first injection.
 32. The method of claim 25, wherein the provision of the Chlamydia antigen(s) comprises: (a) preparing a pharmaceutical composition comprising at least one polynucleotide having a sequence of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO52:, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO: 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, or SEQ ID NO:68, or fragment thereof; (b) administering the pharmaceutical composition to the animal; and (c) expressing one or more Chlamydia antigens in the animal.
 33. The method of claim 32, wherein the at least one Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25,or SEQ ID NO:27 or an antigenic fragment thereof.
 34. The method of claim 33, wherein the at least one Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:11, SEQ ID NO:15, SEQ ID NO:21, or SEQ ID NO:25, or an antigenic fragment thereof.
 35. The method of claim 32, wherein the at least one Chlamydia antigen has a sequence of SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, or SEQ ID NO:69, or an antigenic fragment thereof.
 36. The method of claim 32, wherein the polynucleotide is administered by a first intramuscular injection or epidermal injection.
 37. The method of claim 36, wherein the polynucleotide is administered by a second intramuscular injection and epidermal injection.
 38. The method of claim 37, wherein the intramuscular injection is at least 1.0 μg to 200 μg of the polynucleotide.
 39. The method of claim 25, wherein the provision of the Chlamydia antigen(s) comprises: (a) preparing a pharmaceutical composition of at least one Chlamydia antigen having a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, or SEQ ID NO:69, or an antigenic fragment thereof; and (b) administering the at least one antigen or fragment into the animal.
 40. The method of claim 39, further defined as comprising preparing a pharmaceutical composition of at least one Chlamydia antigen having a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, or SEQ ID NO:27, or an antigenic fragment thereof.
 41. The method of claim 39, further defined as comprising preparing a pharmaceutical composition of at least one Chlamydia antigen having a sequence of SEQ ID NO:7, SEQ ID NO:11, SEQ ID NO:15, SEQ ID NO:21, or SEQ ID NO:25, or an antigenic fragment thereof.
 42. The method of claim 39, further defined as comprising preparing a pharmaceutical composition of at least one Chlamydia antigen having a sequence of SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, or SEQ ID NO:69, or an antigenic fragment thereof.
 43. The method of claim 25, wherein the animal is a mammal.
 44. The method of claim 42, wherein the animal is a bovine.
 45. The method of claim 43, wherein the animal is a human.
 46. The method of claim 25, wherein the method is effective to induce an immune response against Chlamydia psittaci.
 47. The method of claim 25, wherein the method is effective to induce an immune response against Chlamydia pneumoniae.
 48. The method of claim 25, wherein the method is effective to induce an immune response against a Chlamydia species other than Chlamydia psittaci or Chlamydia pneumoniae.
 49. The method of claim 25, wherein the method is effective to induce an immune response against a non-Chlamydia infection.
 50. The method of claim 25, further comprising administering to the animal an antigen or an antigenic fragment from a Chlamydia species other than Chlamydia psittaci or Chlamydia pneumoniae.
 51. The method of claim 25, further comprising administering to the animal an antigen or an antigenic fragment from a non-Chlamydia species.
 52. A method of obtaining polynucleotide sequences effective for generating an immune response against the genus Chlamydia in an animal comprising: (a) preparing a cloned expression library from fragmented genomic DNA of the genus Chlamydia; (b) administering one or more clones of the library in a pharmaceutically acceptable carrier into the animal in an amount effective to induce an immune response; and (c) selecting from the library the polynucleotide sequences that induce an immune response, wherein the immune response in the animal is protective against Chlamydia infection.
 53. The method of claim 52, further comprising testing the animal for immune resistance against a Chlamydia bacterial infection by challenging the animal with Chlamydia.
 54. The method of claim 52, wherein the genomic DNA is fragmented physically or by restriction enzymes.
 55. The method of claim 54, wherein the fragments are, on average, about 200-1000 base pairs in length.
 56. The method of claim 52, wherein each clone in the library comprises a gene encoding a mouse ubiquitin fusion polypeptide designed to link the expression library polynucleotides to the ubiquitin gene.
 57. The method of claim 52, wherein the library is about 1×10³ to about 1×10⁶ clones.
 58. The method of claim 57, wherein the library is 1×10⁵ clones.
 59. The method of claim 52, wherein about 0.01 μg to about 200 μg of DNA, cDNA or sequenced gene from the clones is administered into the animal.
 60. The method of claim 59, wherein the genomic DNA, cDNA or sequenced gene is introduced by intramuscular injection or epidermal injection.
 61. The method of claim 52, wherein the fragmented genomic DNA, cDNA or sequenced genes of Chlamydia further comprises a promoter operably linked to the DNA that permits expression in a vertebrate animal cell.
 62. A method of preparing antigens that confer protection against infection in a vertebrate animal comprising the steps of: a) preparing a cloned expression library from fragmented genomic DNA of the genus Chlamydia psittaci; (b) administering one or more clones of the library in a pharmaceutically acceptable carrier into the animal in an amount effective to induce an immune response; (c) selecting from the library the polynucleotide sequences that induce an immune response and expressing the polynucleotide sequences in cell culture; and (d) purifying the polypeptide(s) expressed in the cell culture.
 63. The method of claim 62, further comprising testing the animal for immune resistance against infection by challenging the animal.
 64. The method of claim 63, wherein the animal is challenged with Chlamydia psittaci.
 65. A method of preparing antibodies against a Chlamydia antigen comprising the steps of: (a) identifying a Chlamydia antigen that confers immune resistance against Chlamydia bacterial infection when challenged with the Chlamydia species in which the antigen was prepared; (b) generating an immune response in a vertebrate animal with the antigen identified in step (a); and (c) obtaining antibodies produced in the animal.
 66. A method of assaying for the presence of Chlamydia infection in a vertebrate animal comprising: (a) obtaining an antibody directed against a Chlamydia antigen; (b) obtaining a sample from the animal; (c) admixing the antibody with the sample; and (d) assaying the sample for antigen-antibody binding, wherein the antigen-antibody binding indicates Chlamydia infection in the animal.
 67. The method of claim 66, wherein the antibody directed against the antigen is further defined as a polyclonal antibody.
 68. The method of claim 66, wherein the antibody directed against the antigen is further defined as a monoclonal antibody.
 69. The method of claim 66, wherein the Chlamydia antigen has a sequence of SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, or SEQ ID NO:61, or an antigenic fragment thereof.
 70. The method of claim 66, wherein the Chlamydia antigen has a sequence of SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, or SEQ ID NO:69, or an antigenic fragment thereof.
 71. The method of claim 66, wherein assaying the sample for antigen-antibody binding is by precipitin reaction, radioimmunoassay, ELISA, Western blot or immunofluorescence.
 72. A kit for assaying a Chlamydia infection comprising, in a suitable container means: (a) a pharmaceutically acceptable carrier; and (b) an antibody directed against a Chlamydia antigen.
 73. A method of testing for antigens for a first disease state or infectious agent comprising: (a) determining an antigenic polypeptide or a nucleic acid encoding an antigenic polypeptide from a second disease state or infectious agent; (b) obtaining a homolog of the antigenic polypeptide or a nucleic acid encoding an antigenic polypeptide from a second disease state or infectious agent for the first disease state or infectious agent; (c) testing the homology to see if it is an antigenic polypeptide or a nucleic acid encoding an antigenic polypeptide for the first disease state or infectious agent. 